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	<id>https://proteopedia.org/api.php?action=feedcontributions&amp;feedformat=atom&amp;user=Dami+Adebambo</id>
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		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620417</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620417"/>
		<updated>2012-11-29T15:51:47Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Cellulases&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). Particularly interesting among this group of enzymes are the ones produced by thermophilic bacteria e.g. the beta -1,4-glucanase (EC 3.2.1.4)from Alicyclobacillus acidocaldarius (Aa_Cel9A), a thermoacidophilic Gram-positive bacterium, displays a temperature optimum of 343 K and a pH optimum of 5.5 (Eckert et al.,2002). Enzymes that can resist higher temperatures and a range of pHs are required since heat and/or chemical pretreatment processes are currently used to remove lignin to expose cellulose to cellulases (Sticklen, 2008)&lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure - the endoglucanase complex&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, the 59kDa endoglucanase is mostly found in the form of a complex that is made up of two to three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. The catalytic module of members of GH family 9 shows an (alpha/alpha)6-barrel structure. The 12 alpha-helices display an alternating connection pattern between outer and inner helices, as is common in (alpha/alpha)6-barrel structures (Parsiegla et al., 1998). The barrel is formed by the parallel inner helices 2, 4, 6, 8, 10 and 12. Besides the 12 alpha-helices, the catalytic module of Aa_Cel9A shows two antiparallel beta-strands and three short alpha-helices which are structurally conserved throughout the family 9 cellulases.A loop of the protein chain forms a tunnel that encloses the &amp;lt;scene name=&#039;Sandbox_Reserved_655/Active_site/1&#039;&amp;gt;active site&amp;lt;/scene&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
[[Image:Active site.jpg | thumb]]&lt;br /&gt;
This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).[[Image:CBM.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). &lt;br /&gt;
&lt;br /&gt;
[[Image:Quartenary.jpg]]&lt;br /&gt;
&lt;br /&gt;
Some features that may be important for thermostability are the fraction of buried atoms, accessible surface area, and lengths of loops connecting the secondary structures elements ( [Chan et al., 1995] and [Russell et al., 1994])&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
&lt;br /&gt;
Cation Exchange Chromatography,Gel filtration chromatography&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
X-ray-diffraction, molecular-replacement method using the program PHASER &lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
[[Image:Hydrolysis.jpeg]]&lt;br /&gt;
&lt;br /&gt;
[[Image:Endoglucanase Mechanism.jpeg]]&lt;br /&gt;
&lt;br /&gt;
The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). &lt;br /&gt;
The CBM &amp;quot;pulls up&amp;quot; the chain and feeds it into the catalytic domain. The CBM&#039;s hydrophoic binding site of three tyrosines remains in contact with the surface throughout the reaction but can freely move translationally. The CBM undergoes a structural conformation after the substrate is in place. The fourth tyrosine (Y13) unfolds from within the CBM and forms a van der Waals interaction with the cellulose surface on the other side of the chain, thus encompassing the reducing end. While the rest of the CBM structure remains fairly rigid because of hydrogen bonds (between strand beta-3 and beta-1 and beta-2) and disulfide bridges (between beta-1 and beta-2) that maintain spacing matching that of the cellulose monomers at the binding site, the fourth tyrosine is located on the remainder of a loop of the protein and is more flexible for the induced fit (Nimlos, et al., 2007). Within the active site, Glutamine (212) acts as a catalytic nucleophile while Trypothan (40) fixes the substrate by hydrophoic interaction at the entrance of the active site tunnel. Similar to myosin and other motor proteins, the enzyme complex is driven by the hydrolysis of the glycosidic bond of cellulose (like phosphate bonds in ATP) as a source of energy for movement along their substrate (Igarashi, et al. 2009).The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
Cellulases represent the third largest class of industrial enzymes worldwide because of their use in cotton processing, paper recycling, as detergent enzymes, in juice extraction, and as animal feed additives. The use of cellulases for the production of renewable fuels from lignocellulosic biomass has the potential to create another large industrial consumer of this class of enzymes (Wilson, 2009).&lt;br /&gt;
[[Image:Biofuel.jpg]]&lt;br /&gt;
&lt;br /&gt;
The growing global demand for energy and the environmental problems caused by the burning of fossil fuels have spurred several efforts to develop renewable alternative fuels (Sticklen, 2008). Global climate change will continue to occur due to the increasing effect of carbon emissions in the atmosphere and political clashes will continue to grow over the control and allocation of these depleting resources, and the costs of these fuels will undoubtedly continue to rise (Merino S.T., and Cherry, J., 2007). One potential approach to producing biofuels is to use the carbohydrate polymers located in tailored crops, such as corn stover and switchgrass, as a source of fermentable sugars ( [Sheehan and Himmel, 1999] and [Simmons et al., 2008]). Cellulose is the main polymer of this biomass and the largest organic carbon reservoir on earth (Festucci-Buselli et al., 2007). Physical and/or chemical pretreatment processes that disrupt the hemicellulose–lignin–cellulose complex in plant cell walls are currently used to make the cellulose accessible to cellulases ( [Sheehan and Himmel, 1999] and [Parsiegla et al., 2008]). In order to make cost-effective biofuels, stable cellulolytic enzymes with high activity in post-pretreatment conditions are essential at an industrial scale of production ( [Wilson, 2009] and [Mahadevan et al., 2008]).The bioconversion process uses enzymes such as endoglucanase to break down cellulose into sugars that can be fermented into ethanol (Figure 6) (Wen, et al., 2009.  Researchers have been looking to engineer microorganisms to withstand the harsh conditions of the process and to produce the necessary enzymes abundantly. It is necessary to understand these enzymes more fully and to improve them via protein engineering so that biomass can be efficiently and inexpensively converted into biofuels.)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) Schubot, F. D., Kataeva, I.A., Chang, J., Shah, A.K. , Ljungdahl, L.G. , Rose, J.P. , Wang, B.C. (2004). Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43, pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) Parsiegla, G., Reverbel, C., Tardif, C., Driguez, H., Haser, R. (2008). Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action. J. Mol. Biol., 375, pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Eckert, K., Zielinski, F., Lo Leggio, L. &amp;amp; Schneider, E. (2002). Appl. Microbiol. Biotechnol. 60, 428–436.&lt;br /&gt;
&lt;br /&gt;
(5) Sticklen, M. B. (2008). Plant genetic engineering for biofuels production: towards affordable cellulosic ethanol Nature, 9 (2008), pp. 433–443.&lt;br /&gt;
&lt;br /&gt;
(6) Nimlos, M.R., Matthews, J.F., Crowley, M.F., Walker, R.C., Chukkapalli, G., Brady, J.W., Adney, W.S., Cleary, J.M., Zhong, L., Himmel, M.E. 2007. Molecular modeling suggests indcued fit of Family 1 carbohydrate-binding modules with a broken-chain cellulose. Protein engineering Design and Selection. 20(4):179-187.&lt;br /&gt;
&lt;br /&gt;
(7) Pilz, I., Schwarz, E. Kilburn, D.G., Miller, R.C. Jr., Warren, R.A.J, Gilkes, N.R. 1990. The tertiary structure of a bacterial cellulase determined by angle X-ray-scattering analysis. Biochem. J. 271:277-280.&lt;br /&gt;
&lt;br /&gt;
(8) Wen, F., Nair, N.U., Zhao, H. 2009. Protein engineering in designing tailored enzymes and microorganisms for biofuels production. Current Opinion in Biotechnology. 20: 412-419.&lt;br /&gt;
&lt;br /&gt;
(9) Zhao, X., Rignall, T.R., McCabe, C., Adney, W.S., Himmel, M.E. 2008. Molecular simulation evidence for processive motion of Tricoderma reesei Cel7A during cellulose depolymerization. Chemical Physics Letters. 460: 284-288.&lt;br /&gt;
&lt;br /&gt;
(10) Zhong, L., Matthews, J.F., Hansen, P.I., Crowley, M.F., Cleary, J.M., Walker, R.C., Nimlos, M.R., Brooks III, C.L., Adney, W.S., Himmel, M.E., Brady, J.W. 2009. Computational simulations of the Trichoderma reesei cellobiohydrolase I acting on microcrystalline cellulose 1beta: the enzyme-substrate complex. Carbohydrate Research. 344(15):1984-1992&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=File:Hydrolysis.jpeg&amp;diff=1620416</id>
		<title>File:Hydrolysis.jpeg</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=File:Hydrolysis.jpeg&amp;diff=1620416"/>
		<updated>2012-11-29T15:50:17Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620415</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620415"/>
		<updated>2012-11-29T15:28:44Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Cellulases&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). Particularly interesting among this group of enzymes are the ones produced by thermophilic bacteria e.g. the beta -1,4-glucanase (EC 3.2.1.4)from Alicyclobacillus acidocaldarius (Aa_Cel9A), a thermoacidophilic Gram-positive bacterium, displays a temperature optimum of 343 K and a pH optimum of 5.5 (Eckert et al.,2002). Enzymes that can resist higher temperatures and a range of pHs are required since heat and/or chemical pretreatment processes are currently used to remove lignin to expose cellulose to cellulases (Sticklen, 2008)&lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure - the endoglucanase complex&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, the 59kDa endoglucanase is mostly found in the form of a complex that is made up of two to three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. The catalytic module of members of GH family 9 shows an (alpha/alpha)6-barrel structure. The 12 alpha-helices display an alternating connection pattern between outer and inner helices, as is common in (alpha/alpha)6-barrel structures (Parsiegla et al., 1998). The barrel is formed by the parallel inner helices 2, 4, 6, 8, 10 and 12. Besides the 12 alpha-helices, the catalytic module of Aa_Cel9A shows two antiparallel beta-strands and three short alpha-helices which are structurally conserved throughout the family 9 cellulases.A loop of the protein chain forms a tunnel that encloses the &amp;lt;scene name=&#039;Sandbox_Reserved_655/Active_site/1&#039;&amp;gt;active site&amp;lt;/scene&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
[[Image:Active site.jpg | thumb]]&lt;br /&gt;
This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).[[Image:CBM.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). &lt;br /&gt;
&lt;br /&gt;
[[Image:Quartenary.jpg]]&lt;br /&gt;
&lt;br /&gt;
Some features that may be important for thermostability are the fraction of buried atoms, accessible surface area, and lengths of loops connecting the secondary structures elements ( [Chan et al., 1995] and [Russell et al., 1994])&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
&lt;br /&gt;
Cation Exchange Chromatography,Gel filtration chromatography&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
X-ray-diffraction, molecular-replacement method using the program PHASER &lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
[[Image:Endoglucanase Mechanism.jpeg]]&lt;br /&gt;
&lt;br /&gt;
The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). &lt;br /&gt;
The CBM &amp;quot;pulls up&amp;quot; the chain and feeds it into the catalytic domain. The CBM&#039;s hydrophoic binding site of three tyrosines remains in contact with the surface throughout the reaction but can freely move translationally. The CBM undergoes a structural conformation after the substrate is in place. The fourth tyrosine (Y13) unfolds from within the CBM and forms a van der Waals interaction with the cellulose surface on the other side of the chain, thus encompassing the reducing end. While the rest of the CBM structure remains fairly rigid because of hydrogen bonds (between strand beta-3 and beta-1 and beta-2) and disulfide bridges (between beta-1 and beta-2) that maintain spacing matching that of the cellulose monomers at the binding site, the fourth tyrosine is located on the remainder of a loop of the protein and is more flexible for the induced fit (Nimlos, et al., 2007). Within the active site, Glutamine (212) acts as a catalytic nucleophile while Trypothan (40) fixes the substrate by hydrophoic interaction at the entrance of the active site tunnel. Similar to myosin and other motor proteins, the enzyme complex is driven by the hydrolysis of the glycosidic bond of cellulose (like phosphate bonds in ATP) as a source of energy for movement along their substrate (Igarashi, et al. 2009).The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
Cellulases represent the third largest class of industrial enzymes worldwide because of their use in cotton processing, paper recycling, as detergent enzymes, in juice extraction, and as animal feed additives. The use of cellulases for the production of renewable fuels from lignocellulosic biomass has the potential to create another large industrial consumer of this class of enzymes (Wilson, 2009).&lt;br /&gt;
[[Image:Biofuel.jpg]]&lt;br /&gt;
&lt;br /&gt;
The growing global demand for energy and the environmental problems caused by the burning of fossil fuels have spurred several efforts to develop renewable alternative fuels (Sticklen, 2008). Global climate change will continue to occur due to the increasing effect of carbon emissions in the atmosphere and political clashes will continue to grow over the control and allocation of these depleting resources, and the costs of these fuels will undoubtedly continue to rise (Merino S.T., and Cherry, J., 2007). One potential approach to producing biofuels is to use the carbohydrate polymers located in tailored crops, such as corn stover and switchgrass, as a source of fermentable sugars ( [Sheehan and Himmel, 1999] and [Simmons et al., 2008]). Cellulose is the main polymer of this biomass and the largest organic carbon reservoir on earth (Festucci-Buselli et al., 2007). Physical and/or chemical pretreatment processes that disrupt the hemicellulose–lignin–cellulose complex in plant cell walls are currently used to make the cellulose accessible to cellulases ( [Sheehan and Himmel, 1999] and [Parsiegla et al., 2008]). In order to make cost-effective biofuels, stable cellulolytic enzymes with high activity in post-pretreatment conditions are essential at an industrial scale of production ( [Wilson, 2009] and [Mahadevan et al., 2008]).The bioconversion process uses enzymes such as endoglucanase to break down cellulose into sugars that can be fermented into ethanol (Figure 6) (Wen, et al., 2009.  Researchers have been looking to engineer microorganisms to withstand the harsh conditions of the process and to produce the necessary enzymes abundantly. It is necessary to understand these enzymes more fully and to improve them via protein engineering so that biomass can be efficiently and inexpensively converted into biofuels.)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) Schubot, F. D., Kataeva, I.A., Chang, J., Shah, A.K. , Ljungdahl, L.G. , Rose, J.P. , Wang, B.C. (2004). Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43, pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) Parsiegla, G., Reverbel, C., Tardif, C., Driguez, H., Haser, R. (2008). Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action. J. Mol. Biol., 375, pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Eckert, K., Zielinski, F., Lo Leggio, L. &amp;amp; Schneider, E. (2002). Appl. Microbiol. Biotechnol. 60, 428–436.&lt;br /&gt;
&lt;br /&gt;
(5) Sticklen, M. B. (2008). Plant genetic engineering for biofuels production: towards affordable cellulosic ethanol Nature, 9 (2008), pp. 433–443.&lt;br /&gt;
&lt;br /&gt;
(6) Nimlos, M.R., Matthews, J.F., Crowley, M.F., Walker, R.C., Chukkapalli, G., Brady, J.W., Adney, W.S., Cleary, J.M., Zhong, L., Himmel, M.E. 2007. Molecular modeling suggests indcued fit of Family 1 carbohydrate-binding modules with a broken-chain cellulose. Protein engineering Design and Selection. 20(4):179-187.&lt;br /&gt;
&lt;br /&gt;
(7) Pilz, I., Schwarz, E. Kilburn, D.G., Miller, R.C. Jr., Warren, R.A.J, Gilkes, N.R. 1990. The tertiary structure of a bacterial cellulase determined by angle X-ray-scattering analysis. Biochem. J. 271:277-280.&lt;br /&gt;
&lt;br /&gt;
(8) Wen, F., Nair, N.U., Zhao, H. 2009. Protein engineering in designing tailored enzymes and microorganisms for biofuels production. Current Opinion in Biotechnology. 20: 412-419.&lt;br /&gt;
&lt;br /&gt;
(9) Zhao, X., Rignall, T.R., McCabe, C., Adney, W.S., Himmel, M.E. 2008. Molecular simulation evidence for processive motion of Tricoderma reesei Cel7A during cellulose depolymerization. Chemical Physics Letters. 460: 284-288.&lt;br /&gt;
&lt;br /&gt;
(10) Zhong, L., Matthews, J.F., Hansen, P.I., Crowley, M.F., Cleary, J.M., Walker, R.C., Nimlos, M.R., Brooks III, C.L., Adney, W.S., Himmel, M.E., Brady, J.W. 2009. Computational simulations of the Trichoderma reesei cellobiohydrolase I acting on microcrystalline cellulose 1beta: the enzyme-substrate complex. Carbohydrate Research. 344(15):1984-1992&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620414</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620414"/>
		<updated>2012-11-29T15:26:45Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Cellulases&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). Particularly interesting among this group of enzymes are the ones produced by thermophilic bacteria e.g. the beta -1,4-glucanase (EC 3.2.1.4)from Alicyclobacillus acidocaldarius (Aa_Cel9A), a thermoacidophilic Gram-positive bacterium, displays a temperature optimum of 343 K and a pH optimum of 5.5 (Eckert et al.,2002). Enzymes that can resist higher temperatures and a range of pHs are required since heat and/or chemical pretreatment processes are currently used to remove lignin to expose cellulose to cellulases (Sticklen, 2008)&lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure - the endoglucanase complex&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, the 59kDa endoglucanase is mostly found in the form of a complex that is made up of two to three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. The catalytic module of members of GH family 9 shows an (alpha/alpha)6-barrel structure. The 12 alpha-helices display an alternating connection pattern between outer and inner helices, as is common in (alpha/alpha)6-barrel structures (Parsiegla et al., 1998). The barrel is formed by the parallel inner helices 2, 4, 6, 8, 10 and 12. Besides the 12 alpha-helices, the catalytic module of Aa_Cel9A shows two antiparallel beta-strands and three short alpha-helices which are structurally conserved throughout the family 9 cellulases.A loop of the protein chain forms a tunnel that encloses the &amp;lt;scene name=&#039;Sandbox_Reserved_655/Active_site/1&#039;&amp;gt;active site&amp;lt;/scene&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
[[Image:Active site.jpg | thumb]]&lt;br /&gt;
This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).[[Image:CBM.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). &lt;br /&gt;
&lt;br /&gt;
[[Image:Quartenary.jpg]]&lt;br /&gt;
&lt;br /&gt;
Some features that may be important for thermostability are the fraction of buried atoms, accessible surface area, and lengths of loops connecting the secondary structures elements ( [Chan et al., 1995] and [Russell et al., 1994])&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
&lt;br /&gt;
Cation Exchange Chromatography,Gel filtration chromatography&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
X-ray-diffraction, molecular-replacement method using the program PHASER &lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
[[Image:Endoglucanase Mechanism.jpeg]]&lt;br /&gt;
&lt;br /&gt;
The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). &lt;br /&gt;
The CBM &amp;quot;pulls up&amp;quot; the chain and feeds it into the catalytic domain. The CBM&#039;s hydrophoic binding site of three tyrosines remains in contact with the surface throughout the reaction but can freely move translationally. The CBM undergoes a structural conformation after the substrate is in place. The fourth tyrosine (Y13) unfolds from within the CBM and forms a van der Waals interaction with the cellulose surface on the other side of the chain, thus encompassing the reducing end. While the rest of the CBM structure remains fairly rigid because of hydrogen bonds (between strand beta-3 and beta-1 and beta-2) and disulfide bridges (between beta-1 and beta-2) that maintain spacing matching that of the cellulose monomers at the binding site, the fourth tyrosine is located on the remainder of a loop of the protein and is more flexible for the induced fit (Nimlos, et al., 2007). Within the active site, Glutamine (212) acts as a catalytic nucleophile while Trypothan (40) fixes the substrate by hydrophoic interaction at the entrance of the active site tunnel. Similar to myosin and other motor proteins, the enzyme complex is driven by the hydrolysis of the glycosidic bond of cellulose (like phosphate bonds in ATP) as a source of energy for movement along their substrate (Igarashi, et al. 2009).The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
Cellulases represent the third largest class of industrial enzymes worldwide because of their use in cotton processing, paper recycling, as detergent enzymes, in juice extraction, and as animal feed additives. The use of cellulases for the production of renewable fuels from lignocellulosic biomass has the potential to create another large industrial consumer of this class of enzymes (Wilson, 2009).&lt;br /&gt;
[[Image:Biofuel.jpg]]&lt;br /&gt;
&lt;br /&gt;
The growing global demand for energy and the environmental problems caused by the burning of fossil fuels have spurred several efforts to develop renewable alternative fuels (Sticklen, 2008). Global climate change will continue to occur due to the increasing effect of carbon emissions in the atmosphere and political clashes will continue to grow over the control and allocation of these depleting resources, and the costs of these fuels will undoubtedly continue to rise (Merino S.T., and Cherry, J., 2007). One potential approach to producing biofuels is to use the carbohydrate polymers located in tailored crops, such as corn stover and switchgrass, as a source of fermentable sugars ( [Sheehan and Himmel, 1999] and [Simmons et al., 2008]). Cellulose is the main polymer of this biomass and the largest organic carbon reservoir on earth (Festucci-Buselli et al., 2007). Physical and/or chemical pretreatment processes that disrupt the hemicellulose–lignin–cellulose complex in plant cell walls are currently used to make the cellulose accessible to cellulases ( [Sheehan and Himmel, 1999] and [Parsiegla et al., 2008]). In order to make cost-effective biofuels, stable cellulolytic enzymes with high activity in post-pretreatment conditions are essential at an industrial scale of production ( [Wilson, 2009] and [Mahadevan et al., 2008]).The bioconversion process uses enzymes such as endoglucanase to break down cellulose into sugars that can be fermented into ethanol (Figure 6) (Wen, et al., 2009.  Researchers have been looking to engineer microorganisms to withstand the harsh conditions of the process and to produce the necessary enzymes abundantly. It is necessary to understand these enzymes more fully and to improve them via protein engineering so that biomass can be efficiently and inexpensively converted into biofuels.)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) Schubot, F. D., Kataeva, I.A., Chang, J., Shah, A.K. , Ljungdahl, L.G. , Rose, J.P. , Wang, B.C. (2004). Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43, pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) Parsiegla, G., Reverbel, C., Tardif, C., Driguez, H., Haser, R. (2008). Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action. J. Mol. Biol., 375, pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Eckert, K., Zielinski, F., Lo Leggio, L. &amp;amp; Schneider, E. (2002). Appl. Microbiol. Biotechnol. 60, 428–436.&lt;br /&gt;
&lt;br /&gt;
(5) Sticklen, M. B. (2008). Plant genetic engineering for biofuels production: towards affordable cellulosic ethanol Nature, 9 (2008), pp. 433–443.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. al.(1974) A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose. Analytical Biochemistry 61.1: 264-270. &lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=File:Biofuel.jpg&amp;diff=1620413</id>
		<title>File:Biofuel.jpg</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=File:Biofuel.jpg&amp;diff=1620413"/>
		<updated>2012-11-29T15:25:19Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620404</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620404"/>
		<updated>2012-11-29T14:28:39Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Cellulases&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). Particularly interesting among this group of enzymes are the ones produced by thermophilic bacteria e.g. the beta -1,4-glucanase (EC 3.2.1.4)from Alicyclobacillus acidocaldarius (Aa_Cel9A), a thermoacidophilic Gram-positive bacterium, displays a temperature optimum of 343 K and a pH optimum of 5.5 (Eckert et al.,2002). Enzymes that can resist higher temperatures and a range of pHs are required since heat and/or chemical pretreatment processes are currently used to remove lignin to expose cellulose to cellulases (Sticklen, 2008)&lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure - the endoglucanase complex&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, the 59kDa endoglucanase is mostly found in the form of a complex that is made up of two to three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. The catalytic module of members of GH family 9 shows an (alpha/alpha)6-barrel structure. The 12 alpha-helices display an alternating connection pattern between outer and inner helices, as is common in (alpha/alpha)6-barrel structures (Parsiegla et al., 1998). The barrel is formed by the parallel inner helices 2, 4, 6, 8, 10 and 12. Besides the 12 alpha-helices, the catalytic module of Aa_Cel9A shows two antiparallel beta-strands and three short alpha-helices which are structurally conserved throughout the family 9 cellulases.A loop of the protein chain forms a tunnel that encloses the &amp;lt;scene name=&#039;Sandbox_Reserved_655/Active_site/1&#039;&amp;gt;active site&amp;lt;/scene&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
[[Image:Active site.jpg | thumb]]&lt;br /&gt;
This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).[[Image:CBM.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). &lt;br /&gt;
&lt;br /&gt;
[[Image:Quartenary.jpg]]&lt;br /&gt;
&lt;br /&gt;
Some features that may be important for thermostability are the fraction of buried atoms, accessible surface area, and lengths of loops connecting the secondary structures elements ( [Chan et al., 1995] and [Russell et al., 1994])&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
&lt;br /&gt;
Cation Exchange Chromatography,Gel filtration chromatography&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
X-ray-diffraction, molecular-replacement method using the program PHASER &lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
[[Image:Endoglucanase Mechanism.jpeg]]&lt;br /&gt;
&lt;br /&gt;
The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). &lt;br /&gt;
The CBM &amp;quot;pulls up&amp;quot; the chain and feeds it into the catalytic domain. The CBM&#039;s hydrophoic binding site of three tyrosines remains in contact with the surface throughout the reaction but can freely move translationally. The CBM undergoes a structural conformation after the substrate is in place. The fourth tyrosine (Y13) unfolds from within the CBM and forms a van der Waals interaction with the cellulose surface on the other side of the chain, thus encompassing the reducing end. While the rest of the CBM structure remains fairly rigid because of hydrogen bonds (between strand beta-3 and beta-1 and beta-2) and disulfide bridges (between beta-1 and beta-2) that maintain spacing matching that of the cellulose monomers at the binding site, the fourth tyrosine is located on the remainder of a loop of the protein and is more flexible for the induced fit (Nimlos, et al., 2007). Within the active site, Glutamine (212) acts as a catalytic nucleophile while Trypothan (40) fixes the substrate by hydrophoic interaction at the entrance of the active site tunnel. Similar to myosin and other motor proteins, the enzyme complex is driven by the hydrolysis of the glycosidic bond of cellulose (like phosphate bonds in ATP) as a source of energy for movement along their substrate (Igarashi, et al. 2009).The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
Cellulases represent the third largest class of industrial enzymes worldwide because of their use in cotton processing, paper recycling, as detergent enzymes, in juice extraction, and as animal feed additives. The use of cellulases for the production of renewable fuels from lignocellulosic biomass has the potential to create another large industrial consumer of this class of enzymes (Wilson, 2009).&lt;br /&gt;
&lt;br /&gt;
The growing global demand for energy and the environmental problems caused by the burning of fossil fuels have spurred several efforts to develop renewable alternative fuels (Sticklen, 2008). Global climate change will continue to occur due to the increasing effect of carbon emissions in the atmosphere and political clashes will continue to grow over the control and allocation of these depleting resources, and the costs of these fuels will undoubtedly continue to rise (Merino S.T., and Cherry, J., 2007). One potential approach to producing biofuels is to use the carbohydrate polymers located in tailored crops, such as corn stover and switchgrass, as a source of fermentable sugars ( [Sheehan and Himmel, 1999] and [Simmons et al., 2008]). Cellulose is the main polymer of this biomass and the largest organic carbon reservoir on earth (Festucci-Buselli et al., 2007). Physical and/or chemical pretreatment processes that disrupt the hemicellulose–lignin–cellulose complex in plant cell walls are currently used to make the cellulose accessible to cellulases ( [Sheehan and Himmel, 1999] and [Parsiegla et al., 2008]). In order to make cost-effective biofuels, stable cellulolytic enzymes with high activity in post-pretreatment conditions are essential at an industrial scale of production ( [Wilson, 2009] and [Mahadevan et al., 2008]).The bioconversion process uses enzymes such as endoglucanase to break down cellulose into sugars that can be fermented into ethanol (Figure 6) (Wen, et al., 2009.  Researchers have been looking to engineer microorganisms to withstand the harsh conditions of the process and to produce the necessary enzymes abundantly. It is necessary to understand these enzymes more fully and to improve them via protein engineering so that biomass can be efficiently and inexpensively converted into biofuels.)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) Schubot, F. D., Kataeva, I.A., Chang, J., Shah, A.K. , Ljungdahl, L.G. , Rose, J.P. , Wang, B.C. (2004). Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43, pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) Parsiegla, G., Reverbel, C., Tardif, C., Driguez, H., Haser, R. (2008). Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action. J. Mol. Biol., 375, pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Eckert, K., Zielinski, F., Lo Leggio, L. &amp;amp; Schneider, E. (2002). Appl. Microbiol. Biotechnol. 60, 428–436.&lt;br /&gt;
&lt;br /&gt;
(5) Sticklen, M. B. (2008). Plant genetic engineering for biofuels production: towards affordable cellulosic ethanol Nature, 9 (2008), pp. 433–443.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. al.(1974) A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose. Analytical Biochemistry 61.1: 264-270. &lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620403</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620403"/>
		<updated>2012-11-29T14:18:12Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Cellulases&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). Particularly interesting among this group of enzymes are the ones produced by thermophilic bacteria e.g. the beta -1,4-glucanase (EC 3.2.1.4)from Alicyclobacillus acidocaldarius (Aa_Cel9A), a thermoacidophilic Gram-positive bacterium, displays a temperature optimum of 343 K and a pH optimum of 5.5 (Eckert et al.,2002). Enzymes that can resist higher temperatures and a range of pHs are required since heat and/or chemical pretreatment processes are currently used to remove lignin to expose cellulose to cellulases (Sticklen, 2008)&lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure - the endoglucanase complex&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, the 59kDa endoglucanase is mostly found in the form of a complex that is made up of two to three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. The catalytic module of members of GH family 9 shows an (alpha/alpha)6-barrel structure. The 12 alpha-helices display an alternating connection pattern between outer and inner helices, as is common in (alpha/alpha)6-barrel structures (Parsiegla et al., 1998). The barrel is formed by the parallel inner helices 2, 4, 6, 8, 10 and 12. Besides the 12 alpha-helices, the catalytic module of Aa_Cel9A shows two antiparallel beta-strands and three short alpha-helices which are structurally conserved throughout the family 9 cellulases.A loop of the protein chain forms a tunnel that encloses the &amp;lt;scene name=&#039;Sandbox_Reserved_655/Active_site/1&#039;&amp;gt;active site&amp;lt;/scene&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
[[Image:Active site.jpg | thumb]]&lt;br /&gt;
This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).[[Image:CBM.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). &lt;br /&gt;
&lt;br /&gt;
[[Image:Quartenary.jpg]]&lt;br /&gt;
&lt;br /&gt;
Some features that may be important for thermostability are the fraction of buried atoms, accessible surface area, and lengths of loops connecting the secondary structures elements ( [Chan et al., 1995] and [Russell et al., 1994])&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
[[Image:Endoglucanase Mechanism.jpeg]]&lt;br /&gt;
&lt;br /&gt;
The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). &lt;br /&gt;
The CBM &amp;quot;pulls up&amp;quot; the chain and feeds it into the catalytic domain. The CBM&#039;s hydrophoic binding site of three tyrosines remains in contact with the surface throughout the reaction but can freely move translationally. The CBM undergoes a structural conformation after the substrate is in place. The fourth tyrosine (Y13) unfolds from within the CBM and forms a van der Waals interaction with the cellulose surface on the other side of the chain, thus encompassing the reducing end. While the rest of the CBM structure remains fairly rigid because of hydrogen bonds (between strand beta-3 and beta-1 and beta-2) and disulfide bridges (between beta-1 and beta-2) that maintain spacing matching that of the cellulose monomers at the binding site, the fourth tyrosine is located on the remainder of a loop of the protein and is more flexible for the induced fit (Nimlos, et al., 2007). Within the active site, Glutamine (212) acts as a catalytic nucleophile while Trypothan (40) fixes the substrate by hydrophoic interaction at the entrance of the active site tunnel. Similar to myosin and other motor proteins, the enzyme complex is driven by the hydrolysis of the glycosidic bond of cellulose (like phosphate bonds in ATP) as a source of energy for movement along their substrate (Igarashi, et al. 2009).The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
Cellulases represent the third largest class of industrial enzymes worldwide because of their use in cotton processing, paper recycling, as detergent enzymes, in juice extraction, and as animal feed additives. The use of cellulases for the production of renewable fuels from lignocellulosic biomass has the potential to create another large industrial consumer of this class of enzymes (Wilson, 2009).&lt;br /&gt;
&lt;br /&gt;
The growing global demand for energy and the environmental problems caused by the burning of fossil fuels have spurred several efforts to develop renewable alternative fuels (Sticklen, 2008). Global climate change will continue to occur due to the increasing effect of carbon emissions in the atmosphere and political clashes will continue to grow over the control and allocation of these depleting resources, and the costs of these fuels will undoubtedly continue to rise (Merino S.T., and Cherry, J., 2007). One potential approach to producing biofuels is to use the carbohydrate polymers located in tailored crops, such as corn stover and switchgrass, as a source of fermentable sugars ( [Sheehan and Himmel, 1999] and [Simmons et al., 2008]). Cellulose is the main polymer of this biomass and the largest organic carbon reservoir on earth (Festucci-Buselli et al., 2007). Physical and/or chemical pretreatment processes that disrupt the hemicellulose–lignin–cellulose complex in plant cell walls are currently used to make the cellulose accessible to cellulases ( [Sheehan and Himmel, 1999] and [Parsiegla et al., 2008]). In order to make cost-effective biofuels, stable cellulolytic enzymes with high activity in post-pretreatment conditions are essential at an industrial scale of production ( [Wilson, 2009] and [Mahadevan et al., 2008]).The bioconversion process uses enzymes such as endoglucanase to break down cellulose into sugars that can be fermented into ethanol (Figure 6) (Wen, et al., 2009.  Researchers have been looking to engineer microorganisms to withstand the harsh conditions of the process and to produce the necessary enzymes abundantly. It is necessary to understand these enzymes more fully and to improve them via protein engineering so that biomass can be efficiently and inexpensively converted into biofuels.)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== References ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) Schubot, F. D., Kataeva, I.A., Chang, J., Shah, A.K. , Ljungdahl, L.G. , Rose, J.P. , Wang, B.C. (2004). Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43, pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) Parsiegla, G., Reverbel, C., Tardif, C., Driguez, H., Haser, R. (2008). Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action. J. Mol. Biol., 375, pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Eckert, K., Zielinski, F., Lo Leggio, L. &amp;amp; Schneider, E. (2002). Appl. Microbiol. Biotechnol. 60, 428–436.&lt;br /&gt;
&lt;br /&gt;
(5) Sticklen, M. B. (2008). Plant genetic engineering for biofuels production: towards affordable cellulosic ethanol Nature, 9 (2008), pp. 433–443.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. al.(1974) A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose. Analytical Biochemistry 61.1: 264-270. &lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620402</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620402"/>
		<updated>2012-11-29T14:17:16Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Cellulases&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). Particularly interesting among this group of enzymes are the ones produced by thermophilic bacteria e.g. the beta -1,4-glucanase (EC 3.2.1.4)from Alicyclobacillus acidocaldarius (Aa_Cel9A), a thermoacidophilic Gram-positive bacterium, displays a temperature optimum of 343 K and a pH optimum of 5.5 (Eckert et al.,2002). Enzymes that can resist higher temperatures and a range of pHs are required since heat and/or chemical pretreatment processes are currently used to remove lignin to expose cellulose to cellulases (Sticklen, 2008)&lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure - the endoglucanase complex&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, the 59kDa endoglucanase is mostly found in the form of a complex that is made up of two to three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. The catalytic module of members of GH family 9 shows an (alpha/alpha)6-barrel structure. The 12 alpha-helices display an alternating connection pattern between outer and inner helices, as is common in (alpha/alpha)6-barrel structures (Parsiegla et al., 1998). The barrel is formed by the parallel inner helices 2, 4, 6, 8, 10 and 12. Besides the 12 alpha-helices, the catalytic module of Aa_Cel9A shows two antiparallel beta-strands and three short alpha-helices which are structurally conserved throughout the family 9 cellulases.A loop of the protein chain forms a tunnel that encloses the &amp;lt;scene name=&#039;Sandbox_Reserved_655/Active_site/1&#039;&amp;gt;active site&amp;lt;/scene&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
[[Image:Active site.jpg | thumb]]&lt;br /&gt;
This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).[[Image:CBM.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). &lt;br /&gt;
&lt;br /&gt;
[[Image:Quartenary.jpg]]&lt;br /&gt;
&lt;br /&gt;
Some features that may be important for thermostability are the fraction of buried atoms, accessible surface area, and lengths of loops connecting the secondary structures elements ( [Chan et al., 1995] and [Russell et al., 1994])&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
[[Image:Endoglucanase Mechanism.jpeg]]&lt;br /&gt;
&lt;br /&gt;
The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). &lt;br /&gt;
The CBM &amp;quot;pulls up&amp;quot; the chain and feeds it into the catalytic domain. The CBM&#039;s hydrophoic binding site of three tyrosines remains in contact with the surface throughout the reaction but can freely move translationally. The CBM undergoes a structural conformation after the substrate is in place. The fourth tyrosine (Y13) unfolds from within the CBM and forms a van der Waals interaction with the cellulose surface on the other side of the chain, thus encompassing the reducing end. While the rest of the CBM structure remains fairly rigid because of hydrogen bonds (between strand beta-3 and beta-1 and beta-2) and disulfide bridges (between beta-1 and beta-2) that maintain spacing matching that of the cellulose monomers at the binding site, the fourth tyrosine is located on the remainder of a loop of the protein and is more flexible for the induced fit (Nimlos, et al., 2007). Within the active site, Glutamine (212) acts as a catalytic nucleophile while Trypothan (40) fixes the substrate by hydrophoic interaction at the entrance of the active site tunnel. Similar to myosin and other motor proteins, the enzyme complex is driven by the hydrolysis of the glycosidic bond of cellulose (like phosphate bonds in ATP) as a source of energy for movement along their substrate (Igarashi, et al. 2009).The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
Cellulases represent the third largest class of industrial enzymes worldwide because of their use in cotton processing, paper recycling, as detergent enzymes, in juice extraction, and as animal feed additives. The use of cellulases for the production of renewable fuels from lignocellulosic biomass has the potential to create another large industrial consumer of this class of enzymes (Wilson, 2009).&lt;br /&gt;
&lt;br /&gt;
The growing global demand for energy and the environmental problems caused by the burning of fossil fuels have spurred several efforts to develop renewable alternative fuels (Sticklen, 2008). Global climate change will continue to occur due to the increasing effect of carbon emissions in the atmosphere and political clashes will continue to grow over the control and allocation of these depleting resources, and the costs of these fuels will undoubtedly continue to rise (Merino S.T., and Cherry, J., 2007). One potential approach to producing biofuels is to use the carbohydrate polymers located in tailored crops, such as corn stover and switchgrass, as a source of fermentable sugars ( [Sheehan and Himmel, 1999] and [Simmons et al., 2008]). Cellulose is the main polymer of this biomass and the largest organic carbon reservoir on earth (Festucci-Buselli et al., 2007). Physical and/or chemical pretreatment processes that disrupt the hemicellulose–lignin–cellulose complex in plant cell walls are currently used to make the cellulose accessible to cellulases ( [Sheehan and Himmel, 1999] and [Parsiegla et al., 2008]). In order to make cost-effective biofuels, stable cellulolytic enzymes with high activity in post-pretreatment conditions are essential at an industrial scale of production ( [Wilson, 2009] and [Mahadevan et al., 2008]).The bioconversion process uses enzymes such as endoglucanase to break down cellulose into sugars that can be fermented into ethanol (Figure 6) (Wen, et al., 2009.  Researchers have been looking to engineer microorganisms to withstand the harsh conditions of the process and to produce the necessary enzymes abundantly. It is necessary to understand these enzymes more fully and to improve them via protein engineering so that biomass can be efficiently and inexpensively converted into biofuels.)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) Schubot, F. D., Kataeva, I.A., Chang, J., Shah, A.K. , Ljungdahl, L.G. , Rose, J.P. , Wang, B.C. (2004). Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43, pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) Parsiegla, G., Reverbel, C., Tardif, C., Driguez, H., Haser, R. (2008). Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action. J. Mol. Biol., 375, pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Eckert, K., Zielinski, F., Lo Leggio, L. &amp;amp; Schneider, E. (2002). Appl. Microbiol. Biotechnol. 60, 428–436.&lt;br /&gt;
&lt;br /&gt;
(5) Sticklen, M. B. (2008). Plant genetic engineering for biofuels production: towards affordable cellulosic ethanol Nature, 9 (2008), pp. 433–443.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. al.(1974) A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose. Analytical Biochemistry 61.1: 264-270. &lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620401</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620401"/>
		<updated>2012-11-29T13:37:31Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). Particularly interesting among this group of enzymes are the ones produced by thermophilic bacteria e.g. the beta -1,4-glucanase (EC 3.2.1.4)from Alicyclobacillus acidocaldarius (Aa_Cel9A), a thermoacidophilic Gram-positive bacterium, displays a temperature optimum of 343 K and a pH optimum of 5.5 (Eckert et al.,2002). Enzymes that can resist higher temperatures and a range of pHs are required since heat and/or chemical pretreatment processes are currently used to remove lignin to expose cellulose to cellulases (Sticklen, 2008)&lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, the 59kDa endoglucanase is mostly found in the form of a complex that is made up of two to three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. The catalytic module of members of GH family 9 shows an (alpha/alpha)6-barrel structure. The 12 alpha-helices display an alternating connection pattern between outer and inner helices, as is common in (alpha/alpha)6-barrel structures (Parsiegla et al., 1998). The barrel is formed by the parallel inner helices 2, 4, 6, 8, 10 and 12. Besides the 12 alpha-helices, the catalytic module of Aa_Cel9A shows two antiparallel beta-strands and three short alpha-helices which are structurally conserved throughout the family 9 cellulases.A loop of the protein chain forms a tunnel that encloses the &amp;lt;scene name=&#039;Sandbox_Reserved_655/Active_site/1&#039;&amp;gt;active site&amp;lt;/scene&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
[[Image:Active site.jpg | thumb]]&lt;br /&gt;
This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).[[Image:CBM.jpg]]&lt;br /&gt;
&lt;br /&gt;
The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). &lt;br /&gt;
&lt;br /&gt;
[[Image:Quartenary.jpg]]&lt;br /&gt;
&lt;br /&gt;
Some features that may be important for thermostability are the fraction of buried atoms, accessible surface area, and lengths of loops connecting the secondary structures elements ( [Chan et al., 1995] and [Russell et al., 1994])&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
[[Image:Endoglucanase Mechanism.jpeg]]&lt;br /&gt;
&lt;br /&gt;
The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). &lt;br /&gt;
The CBM &amp;quot;pulls up&amp;quot; the chain and feeds it into the catalytic domain. The CBM&#039;s hydrophoic binding site of three tyrosines remains in contact with the surface throughout the reaction but can freely move translationally. The CBM undergoes a structural conformation after the substrate is in place. The fourth tyrosine (Y13) unfolds from within the CBM and forms a van der Waals interaction with the cellulose surface on the other side of the chain, thus encompassing the reducing end. While the rest of the CBM structure remains fairly rigid because of hydrogen bonds (between strand beta-3 and beta-1 and beta-2) and disulfide bridges (between beta-1 and beta-2) that maintain spacing matching that of the cellulose monomers at the binding site, the fourth tyrosine is located on the remainder of a loop of the protein and is more flexible for the induced fit (Nimlos, et al., 2007). Within the active site, Glutamine (212) acts as a catalytic nucleophile while Trypothan (40) fixes the substrate by hydrophoic interaction at the entrance of the active site tunnel. Similar to myosin and other motor proteins, the enzyme complex is driven by the hydrolysis of the glycosidic bond of cellulose (like phosphate bonds in ATP) as a source of energy for movement along their substrate (Igarashi, et al. 2009).The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
Cellulases represent the third largest class of industrial enzymes worldwide because of their use in cotton processing, paper recycling, as detergent enzymes, in juice extraction, and as animal feed additives. The use of cellulases for the production of renewable fuels from lignocellulosic biomass has the potential to create another large industrial consumer of this class of enzymes (Wilson, 2009).&lt;br /&gt;
&lt;br /&gt;
The growing global demand for energy and the environmental problems caused by the burning of fossil fuels have spurred several efforts to develop renewable alternative fuels (Sticklen, 2008). Global climate change will continue to occur due to the increasing effect of carbon emissions in the atmosphere and political clashes will continue to grow over the control and allocation of these depleting resources, and the costs of these fuels will undoubtedly continue to rise (Merino S.T., and Cherry, J., 2007). One potential approach to producing biofuels is to use the carbohydrate polymers located in tailored crops, such as corn stover and switchgrass, as a source of fermentable sugars ( [Sheehan and Himmel, 1999] and [Simmons et al., 2008]). Cellulose is the main polymer of this biomass and the largest organic carbon reservoir on earth (Festucci-Buselli et al., 2007). Physical and/or chemical pretreatment processes that disrupt the hemicellulose–lignin–cellulose complex in plant cell walls are currently used to make the cellulose accessible to cellulases ( [Sheehan and Himmel, 1999] and [Parsiegla et al., 2008]). In order to make cost-effective biofuels, stable cellulolytic enzymes with high activity in post-pretreatment conditions are essential at an industrial scale of production ( [Wilson, 2009] and [Mahadevan et al., 2008]).The bioconversion process uses enzymes such as endoglucanase to break down cellulose into sugars that can be fermented into ethanol (Figure 6) (Wen, et al., 2009.  Researchers have been looking to engineer microorganisms to withstand the harsh conditions of the process and to produce the necessary enzymes abundantly. It is necessary to understand these enzymes more fully and to improve them via protein engineering so that biomass can be efficiently and inexpensively converted into biofuels.)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) Schubot, F. D., Kataeva, I.A., Chang, J., Shah, A.K. , Ljungdahl, L.G. , Rose, J.P. , Wang, B.C. (2004). Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43, pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) Parsiegla, G., Reverbel, C., Tardif, C., Driguez, H., Haser, R. (2008). Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action. J. Mol. Biol., 375, pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Eckert, K., Zielinski, F., Lo Leggio, L. &amp;amp; Schneider, E. (2002). Appl. Microbiol. Biotechnol. 60, 428–436.&lt;br /&gt;
&lt;br /&gt;
(5) Sticklen, M. B. (2008). Plant genetic engineering for biofuels production: towards affordable cellulosic ethanol Nature, 9 (2008), pp. 433–443.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. al.(1974) A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose. Analytical Biochemistry 61.1: 264-270. &lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620325</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620325"/>
		<updated>2012-11-29T07:07:05Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). Particularly interesting among this group of enzymes are the ones produced by thermophilic bacteria e.g. the beta -1,4-glucanase (EC 3.2.1.4)from Alicyclobacillus acidocaldarius (Aa_Cel9A), a thermoacidophilic Gram-positive bacterium, displays a temperature optimum of 343 K and a pH optimum of 5.5 (Eckert et al.,2002). Enzymes that can resist higher temperatures and a range of pHs are required since heat and/or chemical pretreatment processes are currently used to remove lignin to expose cellulose to cellulases (Sticklen, 2008)&lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, the 59kDa endoglucanase is mostly found in the form of a complex that is made up of two to three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. The catalytic module of members of GH family 9 shows an (alpha/alpha)6-barrel structure. The 12 alpha-helices display an alternating connection pattern between outer and inner helices, as is common in (alpha/alpha)6-barrel structures (Parsiegla et al., 1998). The barrel is formed by the parallel inner helices 2, 4, 6, 8, 10 and 12. Besides the 12 alpha-helices, the catalytic module of Aa_Cel9A shows two antiparallel beta-strands and three short alpha-helices which are structurally conserved throughout the family 9 cellulases.A loop of the protein chain forms a tunnel that encloses the &amp;lt;scene name=&#039;Sandbox_Reserved_655/Active_site/1&#039;&amp;gt;active site&amp;lt;/scene&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
[[Image:Active site.jpg | thumb]]&lt;br /&gt;
This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).[[Image:CBM.jpg]]&lt;br /&gt;
&lt;br /&gt;
The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). &lt;br /&gt;
&lt;br /&gt;
[[Image:Quartenary.jpg]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
[[Image:Endoglucanase Mechanism.jpeg]]&lt;br /&gt;
&lt;br /&gt;
The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). &lt;br /&gt;
The CBM &amp;quot;pulls up&amp;quot; the chain and feeds it into the catalytic domain. The CBM&#039;s hydrophoic binding site of three tyrosines remains in contact with the surface throughout the reaction but can freely move translationally. The CBM undergoes a structural conformation after the substrate is in place. The fourth tyrosine (Y13) unfolds from within the CBM and forms a van der Waals interaction with the cellulose surface on the other side of the chain, thus encompassing the reducing end. While the rest of the CBM structure remains fairly rigid because of hydrogen bonds (between strand beta-3 and beta-1 and beta-2) and disulfide bridges (between beta-1 and beta-2) that maintain spacing matching that of the cellulose monomers at the binding site, the fourth tyrosine is located on the remainder of a loop of the protein and is more flexible for the induced fit (Nimlos, et al., 2007). Within the active site, Glutamine (212) acts as a catalytic nucleophile while Trypothan (40) fixes the substrate by hydrophoic interaction at the entrance of the active site tunnel. Similar to myosin and other motor proteins, the enzyme complex is driven by the hydrolysis of the glycosidic bond of cellulose (like phosphate bonds in ATP) as a source of energy for movement along their substrate (Igarashi, et al. 2009).The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
Cellulases represent the third largest class of industrial enzymes worldwide because of their use in cotton processing, paper recycling, as detergent enzymes, in juice extraction, and as animal feed additives. The use of cellulases for the production of renewable fuels from lignocellulosic biomass has the potential to create another large industrial consumer of this class of enzymes (Wilson, 2009).&lt;br /&gt;
&lt;br /&gt;
The growing global demand for energy and the environmental problems caused by the burning of fossil fuels have spurred several efforts to develop renewable alternative fuels (Sticklen, 2008). Global climate change will continue to occur due to the increasing effect of carbon emissions in the atmosphere and political clashes will continue to grow over the control and allocation of these depleting resources, and the costs of these fuels will undoubtedly continue to rise (Merino S.T., and Cherry, J., 2007). One potential approach to producing biofuels is to use the carbohydrate polymers located in tailored crops, such as corn stover and switchgrass, as a source of fermentable sugars ( [Sheehan and Himmel, 1999] and [Simmons et al., 2008]). Cellulose is the main polymer of this biomass and the largest organic carbon reservoir on earth (Festucci-Buselli et al., 2007). Physical and/or chemical pretreatment processes that disrupt the hemicellulose–lignin–cellulose complex in plant cell walls are currently used to make the cellulose accessible to cellulases ( [Sheehan and Himmel, 1999] and [Parsiegla et al., 2008]). In order to make cost-effective biofuels, stable cellulolytic enzymes with high activity in post-pretreatment conditions are essential at an industrial scale of production ( [Wilson, 2009] and [Mahadevan et al., 2008]).The bioconversion process uses enzymes such as endoglucanase to break down cellulose into sugars that can be fermented into ethanol (Figure 6) (Wen, et al., 2009.  Researchers have been looking to engineer microorganisms to withstand the harsh conditions of the process and to produce the necessary enzymes abundantly. It is necessary to understand these enzymes more fully and to improve them via protein engineering so that biomass can be efficiently and inexpensively converted into biofuels.)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) Schubot, F. D., Kataeva, I.A., Chang, J., Shah, A.K. , Ljungdahl, L.G. , Rose, J.P. , Wang, B.C. (2004). Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43, pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) Parsiegla, G., Reverbel, C., Tardif, C., Driguez, H., Haser, R. (2008). Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action. J. Mol. Biol., 375, pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Eckert, K., Zielinski, F., Lo Leggio, L. &amp;amp; Schneider, E. (2002). Appl. Microbiol. Biotechnol. 60, 428–436.&lt;br /&gt;
&lt;br /&gt;
(5) Sticklen, M. B. (2008). Plant genetic engineering for biofuels production: towards affordable cellulosic ethanol Nature, 9 (2008), pp. 433–443.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. al.(1974) A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose. Analytical Biochemistry 61.1: 264-270. &lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620324</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620324"/>
		<updated>2012-11-29T07:03:27Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). Particularly interesting among this group of enzymes are the ones produced by thermophilic bacteria e.g. the beta -1,4-glucanase (EC 3.2.1.4)from Alicyclobacillus acidocaldarius (Aa_Cel9A), a thermoacidophilic Gram-positive bacterium, displays a temperature optimum of 343 K and a pH optimum of 5.5 (Eckert et al.,2002). Enzymes that can resist higher temperatures and a range of pHs are required since heat and/or chemical pretreatment processes are currently used to remove lignin to expose cellulose to cellulases (Sticklen, 2008)&lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, the 59kDa endoglucanase is mostly found in the form of a complex that is made up of two to three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. The catalytic module of members of GH family 9 shows an (alpha/alpha)6-barrel structure. The 12 alpha-helices display an alternating connection pattern between outer and inner helices, as is common in (alpha/alpha)6-barrel structures (Parsiegla et al., 1998). The barrel is formed by the parallel inner helices 2, 4, 6, 8, 10 and 12. Besides the 12 alpha-helices, the catalytic module of Aa_Cel9A shows two antiparallel beta-strands and three short alpha-helices which are structurally conserved throughout the family 9 cellulases.A loop of the protein chain forms a tunnel that encloses the &amp;lt;scene name=&#039;Sandbox_Reserved_655/Active_site/1&#039;&amp;gt;active site&amp;lt;/scene&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
[[Image:Active site.jpg | thumb]]&lt;br /&gt;
This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).[[Image:CBM.jpg]]&lt;br /&gt;
&lt;br /&gt;
The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). &lt;br /&gt;
&lt;br /&gt;
[[Image:Quartenary.jpg]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
[[Image:Endoglucanase Mechanism.jpeg]]&lt;br /&gt;
&lt;br /&gt;
The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). &lt;br /&gt;
The CBM &amp;quot;pulls up&amp;quot; the chain and feeds it into the catalytic domain. The CBM&#039;s hydrophoic binding site of three tyrosines remains in contact with the surface throughout the reaction but can freely move translationally. The CBM undergoes a structural conformation after the substrate is in place. The fourth tyrosine (Y13) unfolds from within the CBM and forms a van der Waals interaction with the cellulose surface on the other side of the chain, thus encompassing the reducing end. While the rest of the CBM structure remains fairly rigid because of hydrogen bonds (between strand beta-3 and beta-1 and beta-2) and disulfide bridges (between beta-1 and beta-2) that maintain spacing matching that of the cellulose monomers at the binding site, the fourth tyrosine is located on the remainder of a loop of the protein and is more flexible for the induced fit (Nimlos, et al., 2007). Within the active site, Glutamine (212) acts as a catalytic nucleophile while Trypothan (40) fixes the substrate by hydrophoic interaction at the entrance of the active site tunnel. Similar to myosin and other motor proteins, the enzyme complex is driven by the hydrolysis of the glycosidic bond of cellulose (like phosphate bonds in ATP) as a source of energy for movement along their substrate (Igarashi, et al. 2009).The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
The growing global demand for energy and the environmental problems caused by the burning of fossil fuels have spurred several efforts to develop renewable alternative fuels (Sticklen, 2008). Global climate change will continue to occur due to the increasing effect of carbon emissions in the atmosphere and political clashes will continue to grow over the control and allocation of these depleting resources, and the costs of these fuels will undoubtedly continue to rise (Merino S.T., and Cherry, J., 2007). One potential approach to producing biofuels is to use the carbohydrate polymers located in tailored crops, such as corn stover and switchgrass, as a source of fermentable sugars ( [Sheehan and Himmel, 1999] and [Simmons et al., 2008]). Cellulose is the main polymer of this biomass and the largest organic carbon reservoir on earth (Festucci-Buselli et al., 2007). Physical and/or chemical pretreatment processes that disrupt the hemicellulose–lignin–cellulose complex in plant cell walls are currently used to make the cellulose accessible to cellulases ( [Sheehan and Himmel, 1999] and [Parsiegla et al., 2008]). In order to make cost-effective biofuels, stable cellulolytic enzymes with high activity in post-pretreatment conditions are essential at an industrial scale of production ( [Wilson, 2009] and [Mahadevan et al., 2008]).The bioconversion process uses enzymes such as endoglucanase to break down cellulose into sugars that can be fermented into ethanol (Figure 6) (Wen, et al., 2009.  Researchers have been looking to engineer microorganisms to withstand the harsh conditions of the process and to produce the necessary enzymes abundantly. It is necessary to understand these enzymes more fully and to improve them via protein engineering so that biomass can be efficiently and inexpensively converted into biofuels.)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) Schubot, F. D., Kataeva, I.A., Chang, J., Shah, A.K. , Ljungdahl, L.G. , Rose, J.P. , Wang, B.C. (2004). Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43, pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) Parsiegla, G., Reverbel, C., Tardif, C., Driguez, H., Haser, R. (2008). Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action. J. Mol. Biol., 375, pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Eckert, K., Zielinski, F., Lo Leggio, L. &amp;amp; Schneider, E. (2002). Appl. Microbiol. Biotechnol. 60, 428–436.&lt;br /&gt;
&lt;br /&gt;
(5) Sticklen, M. B. (2008). Plant genetic engineering for biofuels production: towards affordable cellulosic ethanol Nature, 9 (2008), pp. 433–443.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. al.(1974) A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose. Analytical Biochemistry 61.1: 264-270. &lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620318</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620318"/>
		<updated>2012-11-29T06:46:03Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). Particularly interesting among this group of enzymes are the ones produced by thermophilic bacteria e.g. the beta -1,4-glucanase (EC 3.2.1.4)from Alicyclobacillus acidocaldarius (Aa_Cel9A), a thermoacidophilic Gram-positive bacterium, displays a temperature optimum of 343 K and a pH optimum of 5.5 (Eckert et al.,2002). Enzymes that can resist higher temperatures and a range of pHs are required since heat and/or chemical pretreatment processes are currently used to remove lignin to expose cellulose to cellulases (Sticklen, 2008)&lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, the 59kDa endoglucanase is mostly found in the form of a complex that is made up of two to three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. The catalytic module of members of GH family 9 shows an (alpha/alpha)6-barrel structure. The 12 alpha-helices display an alternating connection pattern between outer and inner helices, as is common in (alpha/alpha)6-barrel structures (Parsiegla et al., 1998). The barrel is formed by the parallel inner helices 2, 4, 6, 8, 10 and 12. Besides the 12 alpha-helices, the catalytic module of Aa_Cel9A shows two antiparallel beta-strands and three short alpha-helices which are structurally conserved throughout the family 9 cellulases.A loop of the protein chain forms a tunnel that encloses the &amp;lt;scene name=&#039;Sandbox_Reserved_655/Active_site/1&#039;&amp;gt;active site&amp;lt;/scene&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
[[Image:Active site.jpg | thumb]]&lt;br /&gt;
This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).[[Image:CBM.jpg]]&lt;br /&gt;
&lt;br /&gt;
The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). &lt;br /&gt;
&lt;br /&gt;
[[Image:Quartenary.jpg]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
[[Image:Endoglucanase Mechanism.jpeg]]&lt;br /&gt;
&lt;br /&gt;
The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). &lt;br /&gt;
The CBM &amp;quot;pulls up&amp;quot; the chain and feeds it into the catalytic domain. The CBM&#039;s hydrophoic binding site of three tyrosines remains in contact with the surface throughout the reaction but can freely move translationally. The CBM undergoes a structural conformation after the substrate is in place. The fourth tyrosine (Y13) unfolds from within the CBM and forms a van der Waals interaction with the cellulose surface on the other side of the chain, thus encompassing the reducing end. While the rest of the CBM structure remains fairly rigid because of hydrogen bonds (between strand beta-3 and beta-1 and beta-2) and disulfide bridges (between beta-1 and beta-2) that maintain spacing matching that of the cellulose monomers at the binding site, the fourth tyrosine is located on the remainder of a loop of the protein and is more flexible for the induced fit (Nimlos, et al., 2007). Within the active site, Glutamine (212) acts as a catalytic nucleophile while Trypothan (40) fixes the substrate by hydrophoic interaction at the entrance of the active site tunnel. Similar to myosin and other motor proteins, the enzyme complex is driven by the hydrolysis of the glycosidic bond of cellulose (like phosphate bonds in ATP) as a source of energy for movement along their substrate (Igarashi, et al. 2009).The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) F.D. Schubot, I.A. Kataeva, J. Chang, A.K. Shah, L.G. Ljungdahl, J.P. Rose, B.-C. Wang. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43 (2004), pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) G. Parsiegla, C. Reverbel, C. Tardif, H. Driguez, R. Haser. Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action&lt;br /&gt;
J. Mol. Biol., 375 (2008), pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Eckert, K., Zielinski, F., Lo Leggio, L. &amp;amp; Schneider, E. (2002). Appl. Microbiol. Biotechnol. 60, 428–436.&lt;br /&gt;
&lt;br /&gt;
(5) Sticklen, M. B. (2008). Nature (London), 9, 433–443.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=File:Endoglucanase_Mechanism.jpeg&amp;diff=1620312</id>
		<title>File:Endoglucanase Mechanism.jpeg</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=File:Endoglucanase_Mechanism.jpeg&amp;diff=1620312"/>
		<updated>2012-11-29T06:25:33Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620309</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620309"/>
		<updated>2012-11-29T06:22:15Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). Particularly interesting among this group of enzymes are the ones produced by thermophilic bacteria e.g. the beta -1,4-glucanase (EC 3.2.1.4)from Alicyclobacillus acidocaldarius (Aa_Cel9A), a thermoacidophilic Gram-positive bacterium, displays a temperature optimum of 343 K and a pH optimum of 5.5 (Eckert et al.,2002). Enzymes that can resist higher temperatures and a range of pHs are required since heat and/or chemical pretreatment processes are currently used to remove lignin to expose cellulose to cellulases (Sticklen, 2008)&lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, the 59kDa endoglucanase is mostly found in the form of a complex that is made up of two to three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. The catalytic module of members of GH family 9 shows an (alpha/alpha)6-barrel structure. The 12 alpha-helices display an alternating connection pattern between outer and inner helices, as is common in (alpha/alpha)6-barrel structures (Parsiegla et al., 1998). The barrel is formed by the parallel inner helices 2, 4, 6, 8, 10 and 12. Besides the 12 alpha-helices, the catalytic module of Aa_Cel9A shows two antiparallel beta-strands and three short alpha-helices which are structurally conserved throughout the family 9 cellulases.A loop of the protein chain forms a tunnel that encloses the &amp;lt;scene name=&#039;Sandbox_Reserved_655/Active_site/1&#039;&amp;gt;active site&amp;lt;/scene&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
[[Image:Active site.jpg | thumb]]&lt;br /&gt;
This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).[[Image:CBM.jpg]]&lt;br /&gt;
&lt;br /&gt;
The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). &lt;br /&gt;
&lt;br /&gt;
[[Image:Quartenary.jpg]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
[[Image:Mechanism.jpg]]&lt;br /&gt;
&lt;br /&gt;
The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). &lt;br /&gt;
The CBM &amp;quot;pulls up&amp;quot; the chain and feeds it into the catalytic domain. The CBM&#039;s hydrophoic binding site of three tyrosines remains in contact with the surface throughout the reaction but can freely move translationally. The CBM undergoes a structural conformation after the substrate is in place. The fourth tyrosine (Y13) unfolds from within the CBM and forms a van der Waals interaction with the cellulose surface on the other side of the chain, thus encompassing the reducing end. While the rest of the CBM structure remains fairly rigid because of hydrogen bonds (between strand beta-3 and beta-1 and beta-2) and disulfide bridges (between beta-1 and beta-2) that maintain spacing matching that of the cellulose monomers at the binding site, the fourth tyrosine is located on the remainder of a loop of the protein and is more flexible for the induced fit (Nimlos, et al., 2007). Within the active site, Glutamine (212) acts as a catalytic nucleophile while Trypothan (40) fixes the substrate by hydrophoic interaction at the entrance of the active site tunnel. Similar to myosin and other motor proteins, the enzyme complex is driven by the hydrolysis of the glycosidic bond of cellulose (like phosphate bonds in ATP) as a source of energy for movement along their substrate (Igarashi, et al. 2009).The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) F.D. Schubot, I.A. Kataeva, J. Chang, A.K. Shah, L.G. Ljungdahl, J.P. Rose, B.-C. Wang. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43 (2004), pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) G. Parsiegla, C. Reverbel, C. Tardif, H. Driguez, R. Haser. Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action&lt;br /&gt;
J. Mol. Biol., 375 (2008), pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Eckert, K., Zielinski, F., Lo Leggio, L. &amp;amp; Schneider, E. (2002). Appl. Microbiol. Biotechnol. 60, 428–436.&lt;br /&gt;
&lt;br /&gt;
(5) Sticklen, M. B. (2008). Nature (London), 9, 433–443.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620246</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620246"/>
		<updated>2012-11-28T23:56:10Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). Particularly interesting among this group of enzymes are the ones produced by thermophilic bacteria e.g. the beta -1,4-glucanase (EC 3.2.1.4)from Alicyclobacillus acidocaldarius (Aa_Cel9A), a thermoacidophilic Gram-positive bacterium, displays a temperature optimum of 343 K and a pH optimum of 5.5 (Eckert et al.,2002). Enzymes that can resist higher temperatures and a range of pHs are required since heat and/or chemical pretreatment processes are currently used to remove lignin to expose cellulose to cellulases (Sticklen, 2008)&lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, the 59kDa endoglucanase is mostly found in the form of a complex that is made up of two to three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. The catalytic module of members of GH family 9 shows an (alpha/alpha)6-barrel structure. The 12 alpha-helices display an alternating connection pattern between outer and inner helices, as is common in (alpha/alpha)6-barrel structures (Parsiegla et al., 1998). The barrel is formed by the parallel inner helices 2, 4, 6, 8, 10 and 12. Besides the 12 alpha-helices, the catalytic module of Aa_Cel9A shows two antiparallel beta-strands and three short alpha-helices which are structurally conserved throughout the family 9 cellulases.A loop of the protein chain forms a tunnel that encloses the &amp;lt;scene name=&#039;Sandbox_Reserved_655/Active_site/1&#039;&amp;gt;active site&amp;lt;/scene&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
[[Image:Active site.jpg | thumb]]&lt;br /&gt;
This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).[[Image:CBM.jpg]]&lt;br /&gt;
&lt;br /&gt;
The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). &lt;br /&gt;
&lt;br /&gt;
[[Image:Quartenary.jpg]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
[[Image:Mechanism.jpg]]&lt;br /&gt;
&lt;br /&gt;
The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). &lt;br /&gt;
The CBM &amp;quot;pulls up&amp;quot; the chain and feeds it into the catalytic domain. The CBM&#039;s hydrophoic binding site of three tyrosines remains in contact with the surface throughout the reaction but can freely move translationally. The CBM undergoes a structural conformation after the substrate is in place. The fourth tyrosine (Y13) unfolds from within the CBM and forms a van der Waals interaction with the cellulose surface on the other side of the chain, thus encompassing the reducing end. While the rest of the CBM structure remains fairly rigid because of hydrogen bonds (between strand beta-3 and beta-1 and beta-2) and disulfide bridges (between beta-1 and beta-2) that maintain spacing matching that of the cellulose monomers at the binding site, the fourth tyrosine is located on the remainder of a loop of the protein and is more flexible for the induced fit (Nimlos, et al., 2007). Within the active site, Glutamine (212) acts as a catalytic nucleophile while Trypothan (40) fixes the substrate by hydrophoic interaction at the entrance of the active site tunnel. Similar to myosin and other motor proteins, the enzyme complex is driven by the hydrolysis of the glycosidic bond of cellulose (like phosphate bonds in ATP) as a source of energy for movement along their substrate (Igarashi, et al. 2009).The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) F.D. Schubot, I.A. Kataeva, J. Chang, A.K. Shah, L.G. Ljungdahl, J.P. Rose, B.-C. Wang. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43 (2004), pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) G. Parsiegla, C. Reverbel, C. Tardif, H. Driguez, R. Haser. Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action&lt;br /&gt;
J. Mol. Biol., 375 (2008), pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Eckert, K., Zielinski, F., Lo Leggio, L. &amp;amp; Schneider, E. (2002). Appl. Microbiol. Biotechnol. 60, 428–436.&lt;br /&gt;
&lt;br /&gt;
(5) Sticklen, M. B. (2008). Nature (London), 9, 433–443.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620245</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620245"/>
		<updated>2012-11-28T23:53:39Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). Particularly interesting among this group of enzymes are the ones produced by thermophilic bacteria e.g. the beta -1,4-glucanase (EC 3.2.1.4)from Alicyclobacillus acidocaldarius (Aa_Cel9A), a thermoacidophilic Gram-positive bacterium, displays a temperature optimum of 343 K and a pH optimum of 5.5 (Eckert et al.,2002). Enzymes that can resist higher temperatures and a range of pHs are required since heat and/or chemical pretreatment processes are currently used to remove lignin to expose cellulose to cellulases (Sticklen, 2008)&lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, the 59kDa endoglucanase is mostly found in the form of a complex that is made up of two to three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. The catalytic module of members of GH family 9 shows an (alpha/alpha)6-barrel structure. The 12 alpha-helices display an alternating connection pattern between outer and inner helices, as is common in (alpha/alpha)6-barrel structures (Parsiegla et al., 1998). The barrel is formed by the parallel inner helices 2, 4, 6, 8, 10 and 12. Besides the 12 alpha-helices, the catalytic module of Aa_Cel9A shows two antiparallel beta-strands and three short alpha-helices which are structurally conserved throughout the family 9 cellulases.A loop of the protein chain forms a tunnel that encloses the &amp;lt;scene name=&#039;Sandbox_Reserved_655/Active_site/1&#039;&amp;gt;active site&amp;lt;/scene&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
[[Image:Active site.jpg | thumb]]&lt;br /&gt;
This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).[[Image:CBM.jpg]]&lt;br /&gt;
&lt;br /&gt;
The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). [[Image:Quartenary.jpg]]&lt;br /&gt;
&lt;br /&gt;
The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face) (Figure 3). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
[[Image:Mechanism.jpg]]&lt;br /&gt;
The CBM &amp;quot;pulls up&amp;quot; the chain and feeds it into the catalytic domain. As mentioned before, the CBM&#039;s hydrophoic binding site of three tyrosines remains in contact with the surface throughout the reaction but can freely move translationally. The CBM undergoes a structural conformation after the substrate is in place. The fourth tyrosine (Y13) unfolds from within the CBM and forms a van der Waals interaction with the cellulose surface on the other side of the chain, thus encompassing the reducing end. While the rest of the CBM structure remains fairly rigid because of hydrogen bonds (between strand beta-3 and beta-1 and beta-2) and disulfide bridges (between beta-1 and beta-2) that maintain spacing matching that of the cellulose monomers at the binding site, the fourth tyrosine is located on the remainder of a loop of the protein and is more flexible for the induced fit (Nimlos, et al., 2007). Within the active site, Glutamine (212) acts as a catalytic nucleophile while Trypothan (40) fixes the substrate by hydrophoic interaction at the entrance of the active site tunnel. Similar to myosin and other motor proteins, the enzyme complex is driven by the hydrolysis of the glycosidic bond of cellulose (like phosphate bonds in ATP) as a source of energy for movement along their substrate (Igarashi, et al. 2009).&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) F.D. Schubot, I.A. Kataeva, J. Chang, A.K. Shah, L.G. Ljungdahl, J.P. Rose, B.-C. Wang. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43 (2004), pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) G. Parsiegla, C. Reverbel, C. Tardif, H. Driguez, R. Haser. Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action&lt;br /&gt;
J. Mol. Biol., 375 (2008), pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Eckert, K., Zielinski, F., Lo Leggio, L. &amp;amp; Schneider, E. (2002). Appl. Microbiol. Biotechnol. 60, 428–436.&lt;br /&gt;
&lt;br /&gt;
(5) Sticklen, M. B. (2008). Nature (London), 9, 433–443.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620244</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620244"/>
		<updated>2012-11-28T23:48:26Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). Particularly interesting among this group of enzymes are the ones produced by thermophilic bacteria e.g. the beta -1,4-glucanase (EC 3.2.1.4)from Alicyclobacillus acidocaldarius (Aa_Cel9A), a thermoacidophilic Gram-positive bacterium, displays a temperature optimum of 343 K and a pH optimum of 5.5 (Eckert et al.,2002). Enzymes that can resist higher temperatures and a range of pHs are required since heat and/or chemical pretreatment processes are currently used to remove lignin to expose cellulose to cellulases (Sticklen, 2008)&lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, the 59kDa endoglucanase is mostly found in the form of a complex that is made up of two to three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. The catalytic module of members of GH family 9 shows an (alpha/alpha)6-barrel structure. The 12 alpha-helices display an alternating connection pattern between outer and inner helices, as is common in (alpha/alpha)6-barrel structures (Parsiegla et al., 1998). The barrel is formed by the parallel inner helices 2, 4, 6, 8, 10 and 12. Besides the 12 alpha-helices, the catalytic module of Aa_Cel9A shows two antiparallel beta-strands and three short alpha-helices which are structurally conserved throughout the family 9 cellulases.A loop of the protein chain forms a tunnel that encloses the &amp;lt;scene name=&#039;Sandbox_Reserved_655/Active_site/1&#039;&amp;gt;active site&amp;lt;/scene&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
[[Image:Active site.jpg | thumb]]&lt;br /&gt;
This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).[[Image:CBM.jpg]]&lt;br /&gt;
&lt;br /&gt;
The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). [[Image:Quartenary.jpg]]&lt;br /&gt;
&lt;br /&gt;
The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face) (Figure 3). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
[[Image:Mechanism.jpg]]&lt;br /&gt;
The CBM &amp;quot;pulls up&amp;quot; the chain and feeds it into the catalytic domain. As mentioned before, the CBM&#039;s hydrophoic binding site of three tyrosines remains in contact with the surface throughout the reaction but can freely move translationally. The CBM undergoes a structural conformation after the substrate is in place. The fourth tyrosine (Y13) unfolds from within the CBM and forms a van der Waals interaction with the cellulose surface on the other side of the chain, thus encompassing the reducing end. While the rest of the CBM structure remains fairly rigid because of hydrogen bonds (between strand beta-3 and beta-1 and beta-2) and disulfide bridges (between beta-1 and beta-2) that maintain spacing matching that of the cellulose monomers at the binding site, the fourth tyrosine is located on the remainder of a loop of the protein and is more flexible for the induced fit (Nimlos, et al., 2007). Within the active site, Glutamine (212) acts as a catalytic nucleophile while Trypothan (40) fixes the substrate by hydrophoic interaction at the entrance of the active site tunnel. Similar to myosin and other motor proteins, the enzyme complex is driven by the hydrolysis of the glycosidic bond of cellulose (like phosphate bonds in ATP) as a source of energy for movement along their substrate (Igarashi, et al. 2009).&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) F.D. Schubot, I.A. Kataeva, J. Chang, A.K. Shah, L.G. Ljungdahl, J.P. Rose, B.-C. Wang. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43 (2004), pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) G. Parsiegla, C. Reverbel, C. Tardif, H. Driguez, R. Haser. Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action&lt;br /&gt;
J. Mol. Biol., 375 (2008), pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Smith, Thomas J., and Peter E. Peterson. &amp;quot;The Structure of Bovine Glutamate Dehydrogenase Provides Insights into the Mechanism of Allostery.&amp;quot; Structure 7.7 (1999): 769-782. Print.&lt;br /&gt;
&lt;br /&gt;
(5) Smith, Emil L, et. all. &amp;quot;Bovine Liver Glutamate Dehydrogenase: Tentative Amino Acid Sequence; Identification of a Reactive Lysine; Nitration of a Specific Tyrosine and Loss of Allosteric Inhibition by Guanosine Triphosphate.&amp;quot; Proceedings of the National Academy of Sciences 67.2 (1970): 724-730. Print.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620243</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620243"/>
		<updated>2012-11-28T23:43:32Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). &lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, the 59kDa endoglucanase is mostly found in the form of a complex that is made up of two to three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. The catalytic module of members of GH family 9 shows an (alpha/alpha)6-barrel structure. The 12 alpha-helices display an alternating connection pattern between outer and inner helices, as is common in (alpha/alpha)6-barrel structures (Parsiegla et al., 1998). The barrel is formed by the parallel inner helices 2, 4, 6, 8, 10 and 12. Besides the 12 alpha-helices, the catalytic module of Aa_Cel9A shows two antiparallel beta-strands and three short alpha-helices which are structurally conserved throughout the family 9 cellulases.A loop of the protein chain forms a tunnel that encloses the &amp;lt;scene name=&#039;Sandbox_Reserved_655/Active_site/1&#039;&amp;gt;active site&amp;lt;/scene&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
[[Image:Active site.jpg | thumb]]&lt;br /&gt;
This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).[[Image:CBM.jpg]]&lt;br /&gt;
&lt;br /&gt;
The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). [[Image:Quartenary.jpg]]&lt;br /&gt;
&lt;br /&gt;
The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face) (Figure 3). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
[[Image:Mechanism.jpg]]&lt;br /&gt;
The CBM &amp;quot;pulls up&amp;quot; the chain and feeds it into the catalytic domain. As mentioned before, the CBM&#039;s hydrophoic binding site of three tyrosines remains in contact with the surface throughout the reaction but can freely move translationally. The CBM undergoes a structural conformation after the substrate is in place. The fourth tyrosine (Y13) unfolds from within the CBM and forms a van der Waals interaction with the cellulose surface on the other side of the chain, thus encompassing the reducing end. While the rest of the CBM structure remains fairly rigid because of hydrogen bonds (between strand beta-3 and beta-1 and beta-2) and disulfide bridges (between beta-1 and beta-2) that maintain spacing matching that of the cellulose monomers at the binding site, the fourth tyrosine is located on the remainder of a loop of the protein and is more flexible for the induced fit (Nimlos, et al., 2007). Within the active site, Glutamine (212) acts as a catalytic nucleophile while Trypothan (40) fixes the substrate by hydrophoic interaction at the entrance of the active site tunnel. Similar to myosin and other motor proteins, the enzyme complex is driven by the hydrolysis of the glycosidic bond of cellulose (like phosphate bonds in ATP) as a source of energy for movement along their substrate (Igarashi, et al. 2009).&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) F.D. Schubot, I.A. Kataeva, J. Chang, A.K. Shah, L.G. Ljungdahl, J.P. Rose, B.-C. Wang. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43 (2004), pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) G. Parsiegla, C. Reverbel, C. Tardif, H. Driguez, R. Haser. Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action&lt;br /&gt;
J. Mol. Biol., 375 (2008), pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Smith, Thomas J., and Peter E. Peterson. &amp;quot;The Structure of Bovine Glutamate Dehydrogenase Provides Insights into the Mechanism of Allostery.&amp;quot; Structure 7.7 (1999): 769-782. Print.&lt;br /&gt;
&lt;br /&gt;
(5) Smith, Emil L, et. all. &amp;quot;Bovine Liver Glutamate Dehydrogenase: Tentative Amino Acid Sequence; Identification of a Reactive Lysine; Nitration of a Specific Tyrosine and Loss of Allosteric Inhibition by Guanosine Triphosphate.&amp;quot; Proceedings of the National Academy of Sciences 67.2 (1970): 724-730. Print.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620242</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620242"/>
		<updated>2012-11-28T23:42:49Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). &lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, the 59kDa endoglucanase is mostly found in the form of a complex that is made up of two to three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. The catalytic module of members of GH family 9 shows an (alpha/alpha)6-barrel structure. The 12 alpha-helices display an alternating connection pattern between outer and inner helices, as is common in (alpha/alpha)6-barrel structures (Parsiegla et al., 1998). The barrel is formed by the parallel inner helices 2, 4, 6, 8, 10 and 12. Besides the 12 alpha-helices, the catalytic module of Aa_Cel9A shows two antiparallel beta-strands and three short alpha-helices which are structurally conserved throughout the family 9 cellulases.A loop of the protein chain forms a tunnel that encloses the &amp;lt;scene name=&#039;Sandbox_Reserved_655/Active_site/1&#039;&amp;gt;active site&amp;lt;/scene&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
[[Image:Active site.jpg]]&lt;br /&gt;
This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).[[Image:CBM.jpg]]&lt;br /&gt;
&lt;br /&gt;
The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). [[Image:Quartenary.jpg]]&lt;br /&gt;
&lt;br /&gt;
The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face) (Figure 3). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
[[Image:Mechanism.jpg]]&lt;br /&gt;
The CBM &amp;quot;pulls up&amp;quot; the chain and feeds it into the catalytic domain. As mentioned before, the CBM&#039;s hydrophoic binding site of three tyrosines remains in contact with the surface throughout the reaction but can freely move translationally. The CBM undergoes a structural conformation after the substrate is in place. The fourth tyrosine (Y13) unfolds from within the CBM and forms a van der Waals interaction with the cellulose surface on the other side of the chain, thus encompassing the reducing end. While the rest of the CBM structure remains fairly rigid because of hydrogen bonds (between strand beta-3 and beta-1 and beta-2) and disulfide bridges (between beta-1 and beta-2) that maintain spacing matching that of the cellulose monomers at the binding site, the fourth tyrosine is located on the remainder of a loop of the protein and is more flexible for the induced fit (Nimlos, et al., 2007). Within the active site, Glutamine (212) acts as a catalytic nucleophile while Trypothan (40) fixes the substrate by hydrophoic interaction at the entrance of the active site tunnel. Similar to myosin and other motor proteins, the enzyme complex is driven by the hydrolysis of the glycosidic bond of cellulose (like phosphate bonds in ATP) as a source of energy for movement along their substrate (Igarashi, et al. 2009).&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) F.D. Schubot, I.A. Kataeva, J. Chang, A.K. Shah, L.G. Ljungdahl, J.P. Rose, B.-C. Wang. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43 (2004), pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) G. Parsiegla, C. Reverbel, C. Tardif, H. Driguez, R. Haser. Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action&lt;br /&gt;
J. Mol. Biol., 375 (2008), pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Smith, Thomas J., and Peter E. Peterson. &amp;quot;The Structure of Bovine Glutamate Dehydrogenase Provides Insights into the Mechanism of Allostery.&amp;quot; Structure 7.7 (1999): 769-782. Print.&lt;br /&gt;
&lt;br /&gt;
(5) Smith, Emil L, et. all. &amp;quot;Bovine Liver Glutamate Dehydrogenase: Tentative Amino Acid Sequence; Identification of a Reactive Lysine; Nitration of a Specific Tyrosine and Loss of Allosteric Inhibition by Guanosine Triphosphate.&amp;quot; Proceedings of the National Academy of Sciences 67.2 (1970): 724-730. Print.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=File:Mechanism.jpg&amp;diff=1620241</id>
		<title>File:Mechanism.jpg</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=File:Mechanism.jpg&amp;diff=1620241"/>
		<updated>2012-11-28T23:42:19Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: uploaded a new version of &amp;quot;Image:Mechanism.jpg&amp;quot;&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620239</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620239"/>
		<updated>2012-11-28T23:37:54Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). &lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, the 59kDa endoglucanase is mostly found in the form of a complex that is made up of two to three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. The catalytic module of members of GH family 9 shows an (alpha/alpha)6-barrel structure. The 12 alpha-helices display an alternating connection pattern between outer and inner helices, as is common in (alpha/alpha)6-barrel structures (Parsiegla et al., 1998). The barrel is formed by the parallel inner helices 2, 4, 6, 8, 10 and 12. Besides the 12 alpha-helices, the catalytic module of Aa_Cel9A shows two antiparallel beta-strands and three short alpha-helices which are structurally conserved throughout the family 9 cellulases.A loop of the protein chain forms a tunnel that encloses the &amp;lt;scene name=&#039;Sandbox_Reserved_655/Active_site/1&#039;&amp;gt;active site&amp;lt;/scene&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
[[Image:Active site.jpg]]&lt;br /&gt;
This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).[[Image:CBM.jpg]]&lt;br /&gt;
&lt;br /&gt;
The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). [[Image:Quartenary.jpg]]&lt;br /&gt;
&lt;br /&gt;
The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face) (Figure 3). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
NH4+  +  α-ketoglutarate  + NADPH  +  2 H+ → glutamate +  NADP+   +  H2O&lt;br /&gt;
::[[Image:glutamatedehydrogenase.jpeg]]&lt;br /&gt;
&lt;br /&gt;
The CBM &amp;quot;pulls up&amp;quot; the chain and feeds it into the catalytic domain. As aforementioned, the CBM&#039;s hydrophoic binding site of three tyrosines remains in contact with the surface throughout the reaction but can freely move translationally. The CBM undergoes a structural conformation after the substrate is in place. The fourth tyrosine (Y13) unfolds from within the CBM and forms a van der Waals interaction with the cellulose surface on the other side of the chain, thus encompassing the reducing end. While the rest of the CBM structure remains fairly rigid because of hydrogen bonds (between strand beta-3 and beta-1 and beta-2) and disulfide bridges (between beta-1 and beta-2) that maintain spacing matching that of the cellulose monomers at the binding site, the fourth tyrosine is located on the remainder of a loop of the protein and is more flexible for the induced fit (Nimlos, et al., 2007). Within the active site, Glutamine (212) acts as a catalytic nucleophile while Trypothan (40) fixes the substrate by hydrophoic interaction at the entrance of the active site tunnel. Similar to myosin and other motor proteins, the enzyme complex is driven by the hydrolysis of the glycosidic bond of cellulose (like phosphate bonds in ATP) as a source of energy for movement along their substrate (Igarashi, et al. 2009).&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) F.D. Schubot, I.A. Kataeva, J. Chang, A.K. Shah, L.G. Ljungdahl, J.P. Rose, B.-C. Wang. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43 (2004), pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) G. Parsiegla, C. Reverbel, C. Tardif, H. Driguez, R. Haser. Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action&lt;br /&gt;
J. Mol. Biol., 375 (2008), pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Smith, Thomas J., and Peter E. Peterson. &amp;quot;The Structure of Bovine Glutamate Dehydrogenase Provides Insights into the Mechanism of Allostery.&amp;quot; Structure 7.7 (1999): 769-782. Print.&lt;br /&gt;
&lt;br /&gt;
(5) Smith, Emil L, et. all. &amp;quot;Bovine Liver Glutamate Dehydrogenase: Tentative Amino Acid Sequence; Identification of a Reactive Lysine; Nitration of a Specific Tyrosine and Loss of Allosteric Inhibition by Guanosine Triphosphate.&amp;quot; Proceedings of the National Academy of Sciences 67.2 (1970): 724-730. Print.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=File:Active_site.jpg&amp;diff=1620238</id>
		<title>File:Active site.jpg</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=File:Active_site.jpg&amp;diff=1620238"/>
		<updated>2012-11-28T23:36:00Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: uploaded a new version of &amp;quot;Image:Active site.jpg&amp;quot;&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620237</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620237"/>
		<updated>2012-11-28T23:29:43Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). &lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, the 59kDa endoglucanase is mostly found in the form of a complex that is made up of two to three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. The catalytic module of members of GH family 9 shows an (alpha/alpha�)6-barrel structure. The 12 �-helices (�1–�12)display an alternating connection pattern between outer and inner helices, as is common in (�alpha/alpha�)6-barrel structures (Parsiegla et al., 1998). The barrel is formed by the parallel inner helices �2, �4, �6, �8, �10 and �12. Besides the 12 �-helices, the catalytic module of Aa_Cel9A shows two antiparallel�-strands and three short �-helices which are structurally conserved throughout the family 9 cellulases.A loop of the protein chain forms a tunnel that encloses the &amp;lt;scene name=&#039;Sandbox_Reserved_655/Active_site/1&#039;&amp;gt;active site&amp;lt;/scene&amp;gt;. &lt;br /&gt;
&lt;br /&gt;
This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).[[Image:CBM.jpg]]&lt;br /&gt;
&lt;br /&gt;
The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). [[Image:Quartenary.jpg]]&lt;br /&gt;
&lt;br /&gt;
The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face) (Figure 3). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
NH4+  +  α-ketoglutarate  + NADPH  +  2 H+ → glutamate +  NADP+   +  H2O&lt;br /&gt;
::[[Image:glutamatedehydrogenase.jpeg]]&lt;br /&gt;
&lt;br /&gt;
The CBM &amp;quot;pulls up&amp;quot; the chain and feeds it into the catalytic domain. As aforementioned, the CBM&#039;s hydrophoic binding site of three tyrosines remains in contact with the surface throughout the reaction but can freely move translationally. The CBM undergoes a structural conformation after the substrate is in place. The fourth tyrosine (Y13) unfolds from within the CBM and forms a van der Waals interaction with the cellulose surface on the other side of the chain, thus encompassing the reducing end. While the rest of the CBM structure remains fairly rigid because of hydrogen bonds (between strand beta-3 and beta-1 and beta-2) and disulfide bridges (between beta-1 and beta-2) that maintain spacing matching that of the cellulose monomers at the binding site, the fourth tyrosine is located on the remainder of a loop of the protein and is more flexible for the induced fit (Nimlos, et al., 2007). Within the active site, Glutamine (212) acts as a catalytic nucleophile while Trypothan (40) fixes the substrate by hydrophoic interaction at the entrance of the active site tunnel. Similar to myosin and other motor proteins, the enzyme complex is driven by the hydrolysis of the glycosidic bond of cellulose (like phosphate bonds in ATP) as a source of energy for movement along their substrate (Igarashi, et al. 2009).&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) F.D. Schubot, I.A. Kataeva, J. Chang, A.K. Shah, L.G. Ljungdahl, J.P. Rose, B.-C. Wang. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43 (2004), pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) G. Parsiegla, C. Reverbel, C. Tardif, H. Driguez, R. Haser. Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action&lt;br /&gt;
J. Mol. Biol., 375 (2008), pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Smith, Thomas J., and Peter E. Peterson. &amp;quot;The Structure of Bovine Glutamate Dehydrogenase Provides Insights into the Mechanism of Allostery.&amp;quot; Structure 7.7 (1999): 769-782. Print.&lt;br /&gt;
&lt;br /&gt;
(5) Smith, Emil L, et. all. &amp;quot;Bovine Liver Glutamate Dehydrogenase: Tentative Amino Acid Sequence; Identification of a Reactive Lysine; Nitration of a Specific Tyrosine and Loss of Allosteric Inhibition by Guanosine Triphosphate.&amp;quot; Proceedings of the National Academy of Sciences 67.2 (1970): 724-730. Print.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620236</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620236"/>
		<updated>2012-11-28T23:18:01Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). &lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, endoglucanase is mostly found in the form of a complex that is made up of three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. A loop of the protein chain forms a tunnel that encloses the &amp;lt;scene name=&#039;Sandbox_Reserved_655/Active_site/1&#039;&amp;gt;active site&amp;lt;/scene&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).[[Image:CBM.jpg]]&lt;br /&gt;
&lt;br /&gt;
The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). [[Image:Quartenary.jpg]]&lt;br /&gt;
&lt;br /&gt;
The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face) (Figure 3). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
NH4+  +  α-ketoglutarate  + NADPH  +  2 H+ → glutamate +  NADP+   +  H2O&lt;br /&gt;
::[[Image:glutamatedehydrogenase.jpeg]]&lt;br /&gt;
&lt;br /&gt;
The CBM &amp;quot;pulls up&amp;quot; the chain and feeds it into the catalytic domain. As aforementioned, the CBM&#039;s hydrophoic binding site of three tyrosines remains in contact with the surface throughout the reaction but can freely move translationally. The CBM undergoes a structural conformation after the substrate is in place. The fourth tyrosine (Y13) unfolds from within the CBM and forms a van der Waals interaction with the cellulose surface on the other side of the chain, thus encompassing the reducing end. While the rest of the CBM structure remains fairly rigid because of hydrogen bonds (between strand beta-3 and beta-1 and beta-2) and disulfide bridges (between beta-1 and beta-2) that maintain spacing matching that of the cellulose monomers at the binding site, the fourth tyrosine is located on the remainder of a loop of the protein and is more flexible for the induced fit (Nimlos, et al., 2007). Within the active site, Glutamine (212) acts as a catalytic nucleophile while Trypothan (40) fixes the substrate by hydrophoic interaction at the entrance of the active site tunnel. Similar to myosin and other motor proteins, the enzyme complex is driven by the hydrolysis of the glycosidic bond of cellulose (like phosphate bonds in ATP) as a source of energy for movement along their substrate (Igarashi, et al. 2009).&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) F.D. Schubot, I.A. Kataeva, J. Chang, A.K. Shah, L.G. Ljungdahl, J.P. Rose, B.-C. Wang. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43 (2004), pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) G. Parsiegla, C. Reverbel, C. Tardif, H. Driguez, R. Haser. Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action&lt;br /&gt;
J. Mol. Biol., 375 (2008), pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Smith, Thomas J., and Peter E. Peterson. &amp;quot;The Structure of Bovine Glutamate Dehydrogenase Provides Insights into the Mechanism of Allostery.&amp;quot; Structure 7.7 (1999): 769-782. Print.&lt;br /&gt;
&lt;br /&gt;
(5) Smith, Emil L, et. all. &amp;quot;Bovine Liver Glutamate Dehydrogenase: Tentative Amino Acid Sequence; Identification of a Reactive Lysine; Nitration of a Specific Tyrosine and Loss of Allosteric Inhibition by Guanosine Triphosphate.&amp;quot; Proceedings of the National Academy of Sciences 67.2 (1970): 724-730. Print.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=File:Quartenary.jpg&amp;diff=1620235</id>
		<title>File:Quartenary.jpg</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=File:Quartenary.jpg&amp;diff=1620235"/>
		<updated>2012-11-28T23:16:28Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620233</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620233"/>
		<updated>2012-11-28T23:12:15Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). &lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, endoglucanase is mostly found in the form of a complex that is made up of three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. A loop of the protein chain forms a tunnel that encloses the &amp;lt;scene name=&#039;Sandbox_Reserved_655/Active_site/1&#039;&amp;gt;active site&amp;lt;/scene&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).[[Image:CBM.jpg]]&lt;br /&gt;
&lt;br /&gt;
The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face) (Figure 3). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
NH4+  +  α-ketoglutarate  + NADPH  +  2 H+ → glutamate +  NADP+   +  H2O&lt;br /&gt;
::[[Image:glutamatedehydrogenase.jpeg]]&lt;br /&gt;
&lt;br /&gt;
The CBM &amp;quot;pulls up&amp;quot; the chain and feeds it into the catalytic domain. As aforementioned, the CBM&#039;s hydrophoic binding site of three tyrosines remains in contact with the surface throughout the reaction but can freely move translationally. The CBM undergoes a structural conformation after the substrate is in place. The fourth tyrosine (Y13) unfolds from within the CBM and forms a van der Waals interaction with the cellulose surface on the other side of the chain, thus encompassing the reducing end. While the rest of the CBM structure remains fairly rigid because of hydrogen bonds (between strand beta-3 and beta-1 and beta-2) and disulfide bridges (between beta-1 and beta-2) that maintain spacing matching that of the cellulose monomers at the binding site, the fourth tyrosine is located on the remainder of a loop of the protein and is more flexible for the induced fit (Nimlos, et al., 2007). Within the active site, Glutamine (212) acts as a catalytic nucleophile while Trypothan (40) fixes the substrate by hydrophoic interaction at the entrance of the active site tunnel. Similar to myosin and other motor proteins, the enzyme complex is driven by the hydrolysis of the glycosidic bond of cellulose (like phosphate bonds in ATP) as a source of energy for movement along their substrate (Igarashi, et al. 2009).&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) F.D. Schubot, I.A. Kataeva, J. Chang, A.K. Shah, L.G. Ljungdahl, J.P. Rose, B.-C. Wang. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43 (2004), pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) G. Parsiegla, C. Reverbel, C. Tardif, H. Driguez, R. Haser. Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action&lt;br /&gt;
J. Mol. Biol., 375 (2008), pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Smith, Thomas J., and Peter E. Peterson. &amp;quot;The Structure of Bovine Glutamate Dehydrogenase Provides Insights into the Mechanism of Allostery.&amp;quot; Structure 7.7 (1999): 769-782. Print.&lt;br /&gt;
&lt;br /&gt;
(5) Smith, Emil L, et. all. &amp;quot;Bovine Liver Glutamate Dehydrogenase: Tentative Amino Acid Sequence; Identification of a Reactive Lysine; Nitration of a Specific Tyrosine and Loss of Allosteric Inhibition by Guanosine Triphosphate.&amp;quot; Proceedings of the National Academy of Sciences 67.2 (1970): 724-730. Print.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620232</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620232"/>
		<updated>2012-11-28T23:07:06Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, endoglucanase is mostly found in the form of a complex that is made up of three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. A loop of the protein chain forms a tunnel that encloses the &amp;lt;scene name=&#039;Sandbox_Reserved_655/Active_site/1&#039;&amp;gt;active site&amp;lt;/scene&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).[[Image:CBM.jpg]]&lt;br /&gt;
&lt;br /&gt;
The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face) (Figure 3). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
NH4+  +  α-ketoglutarate  + NADPH  +  2 H+ → glutamate +  NADP+   +  H2O&lt;br /&gt;
::[[Image:glutamatedehydrogenase.jpeg]]&lt;br /&gt;
&lt;br /&gt;
Glutamate dehydrogenase is important in nitrogen and glutamate metabolism and energy homeostasis. In the reaction above the forward reaction is essential in converting free ammonia and α-ketoglutarate to glutamate, an amino acid that is used for protein synthesis. The reverse reaction is key reaction that links amino acid metabolism with the Tricarboxylic Acid cycle (TCA cycle). Both reactions utilize nicotinamide nucleotide cofactors: NAD+ when nitrogen is released and NADPH when nitrogen is used. Glutamate dehydrogenase is regulated by cell energy charge.  This requires Adenosine triphosphate (ATP) and Guanosine triphosphate (GTP) are positive allosteric effectors for the forward reaction and Adenosine diphosphate (ADP) and Guanosine diphosphate are positive allosteric effectors for the reverse reaction. When the level of ATP is high, conversion of glutamate to α-ketoglurate and other TCA cycle intermediates is limited; when the cellular energy charge is low, glutamate is converted to ammonia and oxidizable TCA cycle intermediates. Glutamate is an important amino acid since it gives an amine group for many transamination reactions, thus, glutamate dehydrogenase is essential in producing this amino acid. (9)&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) F.D. Schubot, I.A. Kataeva, J. Chang, A.K. Shah, L.G. Ljungdahl, J.P. Rose, B.-C. Wang. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43 (2004), pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) G. Parsiegla, C. Reverbel, C. Tardif, H. Driguez, R. Haser. Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action&lt;br /&gt;
J. Mol. Biol., 375 (2008), pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Smith, Thomas J., and Peter E. Peterson. &amp;quot;The Structure of Bovine Glutamate Dehydrogenase Provides Insights into the Mechanism of Allostery.&amp;quot; Structure 7.7 (1999): 769-782. Print.&lt;br /&gt;
&lt;br /&gt;
(5) Smith, Emil L, et. all. &amp;quot;Bovine Liver Glutamate Dehydrogenase: Tentative Amino Acid Sequence; Identification of a Reactive Lysine; Nitration of a Specific Tyrosine and Loss of Allosteric Inhibition by Guanosine Triphosphate.&amp;quot; Proceedings of the National Academy of Sciences 67.2 (1970): 724-730. Print.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=File:CBM.jpg&amp;diff=1620231</id>
		<title>File:CBM.jpg</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=File:CBM.jpg&amp;diff=1620231"/>
		<updated>2012-11-28T23:03:14Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620230</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620230"/>
		<updated>2012-11-28T22:59:21Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, endoglucanase is mostly found in the form of a complex that is made up of three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. A loop of the protein chain forms a tunnel that encloses the &amp;lt;scene name=&#039;Sandbox_Reserved_655/Active_site/1&#039;&amp;gt;active site&amp;lt;/scene&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face) (Figure 3). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
NH4+  +  α-ketoglutarate  + NADPH  +  2 H+ → glutamate +  NADP+   +  H2O&lt;br /&gt;
::[[Image:glutamatedehydrogenase.jpeg]]&lt;br /&gt;
&lt;br /&gt;
Glutamate dehydrogenase is important in nitrogen and glutamate metabolism and energy homeostasis. In the reaction above the forward reaction is essential in converting free ammonia and α-ketoglutarate to glutamate, an amino acid that is used for protein synthesis. The reverse reaction is key reaction that links amino acid metabolism with the Tricarboxylic Acid cycle (TCA cycle). Both reactions utilize nicotinamide nucleotide cofactors: NAD+ when nitrogen is released and NADPH when nitrogen is used. Glutamate dehydrogenase is regulated by cell energy charge.  This requires Adenosine triphosphate (ATP) and Guanosine triphosphate (GTP) are positive allosteric effectors for the forward reaction and Adenosine diphosphate (ADP) and Guanosine diphosphate are positive allosteric effectors for the reverse reaction. When the level of ATP is high, conversion of glutamate to α-ketoglurate and other TCA cycle intermediates is limited; when the cellular energy charge is low, glutamate is converted to ammonia and oxidizable TCA cycle intermediates. Glutamate is an important amino acid since it gives an amine group for many transamination reactions, thus, glutamate dehydrogenase is essential in producing this amino acid. (9)&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) F.D. Schubot, I.A. Kataeva, J. Chang, A.K. Shah, L.G. Ljungdahl, J.P. Rose, B.-C. Wang. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43 (2004), pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) G. Parsiegla, C. Reverbel, C. Tardif, H. Driguez, R. Haser. Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action&lt;br /&gt;
J. Mol. Biol., 375 (2008), pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Smith, Thomas J., and Peter E. Peterson. &amp;quot;The Structure of Bovine Glutamate Dehydrogenase Provides Insights into the Mechanism of Allostery.&amp;quot; Structure 7.7 (1999): 769-782. Print.&lt;br /&gt;
&lt;br /&gt;
(5) Smith, Emil L, et. all. &amp;quot;Bovine Liver Glutamate Dehydrogenase: Tentative Amino Acid Sequence; Identification of a Reactive Lysine; Nitration of a Specific Tyrosine and Loss of Allosteric Inhibition by Guanosine Triphosphate.&amp;quot; Proceedings of the National Academy of Sciences 67.2 (1970): 724-730. Print.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620229</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620229"/>
		<updated>2012-11-28T22:32:53Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, endoglucanase is mostly found in the form of a complex that is made up of three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. A loop of the protein chain forms a tunnel that encloses the &lt;br /&gt;
&amp;lt;scene name=&#039;Sandbox_Reserved_655/Active_site/1&#039;&amp;gt;active site&amp;lt;/scene&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
 This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face) (Figure 3). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
NH4+  +  α-ketoglutarate  + NADPH  +  2 H+ → glutamate +  NADP+   +  H2O&lt;br /&gt;
::[[Image:glutamatedehydrogenase.jpeg]]&lt;br /&gt;
&lt;br /&gt;
Glutamate dehydrogenase is important in nitrogen and glutamate metabolism and energy homeostasis. In the reaction above the forward reaction is essential in converting free ammonia and α-ketoglutarate to glutamate, an amino acid that is used for protein synthesis. The reverse reaction is key reaction that links amino acid metabolism with the Tricarboxylic Acid cycle (TCA cycle). Both reactions utilize nicotinamide nucleotide cofactors: NAD+ when nitrogen is released and NADPH when nitrogen is used. Glutamate dehydrogenase is regulated by cell energy charge.  This requires Adenosine triphosphate (ATP) and Guanosine triphosphate (GTP) are positive allosteric effectors for the forward reaction and Adenosine diphosphate (ADP) and Guanosine diphosphate are positive allosteric effectors for the reverse reaction. When the level of ATP is high, conversion of glutamate to α-ketoglurate and other TCA cycle intermediates is limited; when the cellular energy charge is low, glutamate is converted to ammonia and oxidizable TCA cycle intermediates. Glutamate is an important amino acid since it gives an amine group for many transamination reactions, thus, glutamate dehydrogenase is essential in producing this amino acid. (9)&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) F.D. Schubot, I.A. Kataeva, J. Chang, A.K. Shah, L.G. Ljungdahl, J.P. Rose, B.-C. Wang. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43 (2004), pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) G. Parsiegla, C. Reverbel, C. Tardif, H. Driguez, R. Haser. Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action&lt;br /&gt;
J. Mol. Biol., 375 (2008), pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Smith, Thomas J., and Peter E. Peterson. &amp;quot;The Structure of Bovine Glutamate Dehydrogenase Provides Insights into the Mechanism of Allostery.&amp;quot; Structure 7.7 (1999): 769-782. Print.&lt;br /&gt;
&lt;br /&gt;
(5) Smith, Emil L, et. all. &amp;quot;Bovine Liver Glutamate Dehydrogenase: Tentative Amino Acid Sequence; Identification of a Reactive Lysine; Nitration of a Specific Tyrosine and Loss of Allosteric Inhibition by Guanosine Triphosphate.&amp;quot; Proceedings of the National Academy of Sciences 67.2 (1970): 724-730. Print.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620228</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620228"/>
		<updated>2012-11-28T22:29:19Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, endoglucanase is mostly found in the form of a complex that is made up of three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. A loop of the protein chain forms a tunnel that encloses the &amp;lt;scene name=&#039;Sandbox_Reserved_655/Active_site/1&#039;&amp;gt;active site&amp;lt;/scene&amp;gt;.&lt;br /&gt;
 This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face) (Figure 3). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
NH4+  +  α-ketoglutarate  + NADPH  +  2 H+ → glutamate +  NADP+   +  H2O&lt;br /&gt;
::[[Image:glutamatedehydrogenase.jpeg]]&lt;br /&gt;
&lt;br /&gt;
Glutamate dehydrogenase is important in nitrogen and glutamate metabolism and energy homeostasis. In the reaction above the forward reaction is essential in converting free ammonia and α-ketoglutarate to glutamate, an amino acid that is used for protein synthesis. The reverse reaction is key reaction that links amino acid metabolism with the Tricarboxylic Acid cycle (TCA cycle). Both reactions utilize nicotinamide nucleotide cofactors: NAD+ when nitrogen is released and NADPH when nitrogen is used. Glutamate dehydrogenase is regulated by cell energy charge.  This requires Adenosine triphosphate (ATP) and Guanosine triphosphate (GTP) are positive allosteric effectors for the forward reaction and Adenosine diphosphate (ADP) and Guanosine diphosphate are positive allosteric effectors for the reverse reaction. When the level of ATP is high, conversion of glutamate to α-ketoglurate and other TCA cycle intermediates is limited; when the cellular energy charge is low, glutamate is converted to ammonia and oxidizable TCA cycle intermediates. Glutamate is an important amino acid since it gives an amine group for many transamination reactions, thus, glutamate dehydrogenase is essential in producing this amino acid. (9)&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) F.D. Schubot, I.A. Kataeva, J. Chang, A.K. Shah, L.G. Ljungdahl, J.P. Rose, B.-C. Wang. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43 (2004), pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) G. Parsiegla, C. Reverbel, C. Tardif, H. Driguez, R. Haser. Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action&lt;br /&gt;
J. Mol. Biol., 375 (2008), pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Smith, Thomas J., and Peter E. Peterson. &amp;quot;The Structure of Bovine Glutamate Dehydrogenase Provides Insights into the Mechanism of Allostery.&amp;quot; Structure 7.7 (1999): 769-782. Print.&lt;br /&gt;
&lt;br /&gt;
(5) Smith, Emil L, et. all. &amp;quot;Bovine Liver Glutamate Dehydrogenase: Tentative Amino Acid Sequence; Identification of a Reactive Lysine; Nitration of a Specific Tyrosine and Loss of Allosteric Inhibition by Guanosine Triphosphate.&amp;quot; Proceedings of the National Academy of Sciences 67.2 (1970): 724-730. Print.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620227</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620227"/>
		<updated>2012-11-28T22:01:13Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, endoglucanase is mostly found in the form of a complex that is made up of three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. A loop of the protein chain forms a tunnel that encloses the active site. This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face) (Figure 3). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
NH4+  +  α-ketoglutarate  + NADPH  +  2 H+ → glutamate +  NADP+   +  H2O&lt;br /&gt;
::[[Image:glutamatedehydrogenase.jpeg]]&lt;br /&gt;
&lt;br /&gt;
Glutamate dehydrogenase is important in nitrogen and glutamate metabolism and energy homeostasis. In the reaction above the forward reaction is essential in converting free ammonia and α-ketoglutarate to glutamate, an amino acid that is used for protein synthesis. The reverse reaction is key reaction that links amino acid metabolism with the Tricarboxylic Acid cycle (TCA cycle). Both reactions utilize nicotinamide nucleotide cofactors: NAD+ when nitrogen is released and NADPH when nitrogen is used. Glutamate dehydrogenase is regulated by cell energy charge.  This requires Adenosine triphosphate (ATP) and Guanosine triphosphate (GTP) are positive allosteric effectors for the forward reaction and Adenosine diphosphate (ADP) and Guanosine diphosphate are positive allosteric effectors for the reverse reaction. When the level of ATP is high, conversion of glutamate to α-ketoglurate and other TCA cycle intermediates is limited; when the cellular energy charge is low, glutamate is converted to ammonia and oxidizable TCA cycle intermediates. Glutamate is an important amino acid since it gives an amine group for many transamination reactions, thus, glutamate dehydrogenase is essential in producing this amino acid. (9)&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) F.D. Schubot, I.A. Kataeva, J. Chang, A.K. Shah, L.G. Ljungdahl, J.P. Rose, B.-C. Wang. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43 (2004), pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) G. Parsiegla, C. Reverbel, C. Tardif, H. Driguez, R. Haser. Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action&lt;br /&gt;
J. Mol. Biol., 375 (2008), pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Smith, Thomas J., and Peter E. Peterson. &amp;quot;The Structure of Bovine Glutamate Dehydrogenase Provides Insights into the Mechanism of Allostery.&amp;quot; Structure 7.7 (1999): 769-782. Print.&lt;br /&gt;
&lt;br /&gt;
(5) Smith, Emil L, et. all. &amp;quot;Bovine Liver Glutamate Dehydrogenase: Tentative Amino Acid Sequence; Identification of a Reactive Lysine; Nitration of a Specific Tyrosine and Loss of Allosteric Inhibition by Guanosine Triphosphate.&amp;quot; Proceedings of the National Academy of Sciences 67.2 (1970): 724-730. Print.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620226</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620226"/>
		<updated>2012-11-28T21:44:27Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, endoglucanase is mostly found in the form of a complex that is made up of three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. A loop of the protein chain forms a tunnel that encloses the active site. This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face) (Figure 3). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
[[Image:Image:3vdh_bio_r_500.jpg | thumb]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
NH4+  +  α-ketoglutarate  + NADPH  +  2 H+ → glutamate +  NADP+   +  H2O&lt;br /&gt;
::[[Image:glutamatedehydrogenase.jpeg]]&lt;br /&gt;
&lt;br /&gt;
Glutamate dehydrogenase is important in nitrogen and glutamate metabolism and energy homeostasis. In the reaction above the forward reaction is essential in converting free ammonia and α-ketoglutarate to glutamate, an amino acid that is used for protein synthesis. The reverse reaction is key reaction that links amino acid metabolism with the Tricarboxylic Acid cycle (TCA cycle). Both reactions utilize nicotinamide nucleotide cofactors: NAD+ when nitrogen is released and NADPH when nitrogen is used. Glutamate dehydrogenase is regulated by cell energy charge.  This requires Adenosine triphosphate (ATP) and Guanosine triphosphate (GTP) are positive allosteric effectors for the forward reaction and Adenosine diphosphate (ADP) and Guanosine diphosphate are positive allosteric effectors for the reverse reaction. When the level of ATP is high, conversion of glutamate to α-ketoglurate and other TCA cycle intermediates is limited; when the cellular energy charge is low, glutamate is converted to ammonia and oxidizable TCA cycle intermediates. Glutamate is an important amino acid since it gives an amine group for many transamination reactions, thus, glutamate dehydrogenase is essential in producing this amino acid. (9)&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) F.D. Schubot, I.A. Kataeva, J. Chang, A.K. Shah, L.G. Ljungdahl, J.P. Rose, B.-C. Wang. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43 (2004), pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) G. Parsiegla, C. Reverbel, C. Tardif, H. Driguez, R. Haser. Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action&lt;br /&gt;
J. Mol. Biol., 375 (2008), pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Smith, Thomas J., and Peter E. Peterson. &amp;quot;The Structure of Bovine Glutamate Dehydrogenase Provides Insights into the Mechanism of Allostery.&amp;quot; Structure 7.7 (1999): 769-782. Print.&lt;br /&gt;
&lt;br /&gt;
(5) Smith, Emil L, et. all. &amp;quot;Bovine Liver Glutamate Dehydrogenase: Tentative Amino Acid Sequence; Identification of a Reactive Lysine; Nitration of a Specific Tyrosine and Loss of Allosteric Inhibition by Guanosine Triphosphate.&amp;quot; Proceedings of the National Academy of Sciences 67.2 (1970): 724-730. Print.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620225</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620225"/>
		<updated>2012-11-28T21:40:07Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, endoglucanase is mostly found in the form of a complex that is made up of three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. A loop of the protein chain forms a tunnel that encloses the active site. This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face) (Figure 3). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The figure on the right shows the two domains of GDH.  The orange represent the glutamate binding sites and the blue sites represent the domain involved in assembly of the hexamer.&lt;br /&gt;
&lt;br /&gt;
---&lt;br /&gt;
[[Image:Image:3vdh_bio_r_500.jpg]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
NH4+  +  α-ketoglutarate  + NADPH  +  2 H+ → glutamate +  NADP+   +  H2O&lt;br /&gt;
::[[Image:glutamatedehydrogenase.jpeg]]&lt;br /&gt;
&lt;br /&gt;
Glutamate dehydrogenase is important in nitrogen and glutamate metabolism and energy homeostasis. In the reaction above the forward reaction is essential in converting free ammonia and α-ketoglutarate to glutamate, an amino acid that is used for protein synthesis. The reverse reaction is key reaction that links amino acid metabolism with the Tricarboxylic Acid cycle (TCA cycle). Both reactions utilize nicotinamide nucleotide cofactors: NAD+ when nitrogen is released and NADPH when nitrogen is used. Glutamate dehydrogenase is regulated by cell energy charge.  This requires Adenosine triphosphate (ATP) and Guanosine triphosphate (GTP) are positive allosteric effectors for the forward reaction and Adenosine diphosphate (ADP) and Guanosine diphosphate are positive allosteric effectors for the reverse reaction. When the level of ATP is high, conversion of glutamate to α-ketoglurate and other TCA cycle intermediates is limited; when the cellular energy charge is low, glutamate is converted to ammonia and oxidizable TCA cycle intermediates. Glutamate is an important amino acid since it gives an amine group for many transamination reactions, thus, glutamate dehydrogenase is essential in producing this amino acid. (9)&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) F.D. Schubot, I.A. Kataeva, J. Chang, A.K. Shah, L.G. Ljungdahl, J.P. Rose, B.-C. Wang. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43 (2004), pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) G. Parsiegla, C. Reverbel, C. Tardif, H. Driguez, R. Haser. Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action&lt;br /&gt;
J. Mol. Biol., 375 (2008), pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Smith, Thomas J., and Peter E. Peterson. &amp;quot;The Structure of Bovine Glutamate Dehydrogenase Provides Insights into the Mechanism of Allostery.&amp;quot; Structure 7.7 (1999): 769-782. Print.&lt;br /&gt;
&lt;br /&gt;
(5) Smith, Emil L, et. all. &amp;quot;Bovine Liver Glutamate Dehydrogenase: Tentative Amino Acid Sequence; Identification of a Reactive Lysine; Nitration of a Specific Tyrosine and Loss of Allosteric Inhibition by Guanosine Triphosphate.&amp;quot; Proceedings of the National Academy of Sciences 67.2 (1970): 724-730. Print.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620222</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620222"/>
		<updated>2012-11-28T20:47:00Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, endoglucanase is mostly found in the form of a complex that is made up of three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. A loop of the protein chain forms a tunnel that encloses the active site. This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).The overall shape of the complex looks like a tadpole, with the A and B blocks forming the extended tail and the catalytic domain forming the head (Pilz, et al., 1990). The CBM facilitates the enzyme by binding the complex to the cellulose, thus maintaining the proximity of the enzyme and the substrate. It can also target areas of the cellulose that are specific to the enzyme complex. In addition, the CBM itself can disrupt the structure of the cellulose and thus expose the substrate more to the enzyme. The aromatic amino acid residues and planar architecture of the CBM binding sites are complementary to the hydrophobic sites of cellulose chains (hydrophobic 110 face) (Figure 3). This exposes the beta-D-glucopyranose rings in the chair conformation, which have their alpha and beta faces having either two or three axial hydrogens exposed and ring hydroxyl groups in the equatorial position, allowing the CBMs to bind efficiently (Nimlos, et al., 2007). The thermodynamic forces that drive this interaction is controversial, but most researchers postulate that it comes from the positive entropy when the water molecules are released from the protein and ligand (Boraston, et al., 2004).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The figure on the right shows the two domains of GDH.  The orange represent the glutamate binding sites and the blue sites represent the domain involved in assembly of the hexamer.&lt;br /&gt;
&lt;br /&gt;
[[Image:structure.jpeg]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
NH4+  +  α-ketoglutarate  + NADPH  +  2 H+ → glutamate +  NADP+   +  H2O&lt;br /&gt;
::[[Image:glutamatedehydrogenase.jpeg]]&lt;br /&gt;
&lt;br /&gt;
Glutamate dehydrogenase is important in nitrogen and glutamate metabolism and energy homeostasis. In the reaction above the forward reaction is essential in converting free ammonia and α-ketoglutarate to glutamate, an amino acid that is used for protein synthesis. The reverse reaction is key reaction that links amino acid metabolism with the Tricarboxylic Acid cycle (TCA cycle). Both reactions utilize nicotinamide nucleotide cofactors: NAD+ when nitrogen is released and NADPH when nitrogen is used. Glutamate dehydrogenase is regulated by cell energy charge.  This requires Adenosine triphosphate (ATP) and Guanosine triphosphate (GTP) are positive allosteric effectors for the forward reaction and Adenosine diphosphate (ADP) and Guanosine diphosphate are positive allosteric effectors for the reverse reaction. When the level of ATP is high, conversion of glutamate to α-ketoglurate and other TCA cycle intermediates is limited; when the cellular energy charge is low, glutamate is converted to ammonia and oxidizable TCA cycle intermediates. Glutamate is an important amino acid since it gives an amine group for many transamination reactions, thus, glutamate dehydrogenase is essential in producing this amino acid. (9)&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) F.D. Schubot, I.A. Kataeva, J. Chang, A.K. Shah, L.G. Ljungdahl, J.P. Rose, B.-C. Wang. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43 (2004), pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) G. Parsiegla, C. Reverbel, C. Tardif, H. Driguez, R. Haser. Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action&lt;br /&gt;
J. Mol. Biol., 375 (2008), pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Smith, Thomas J., and Peter E. Peterson. &amp;quot;The Structure of Bovine Glutamate Dehydrogenase Provides Insights into the Mechanism of Allostery.&amp;quot; Structure 7.7 (1999): 769-782. Print.&lt;br /&gt;
&lt;br /&gt;
(5) Smith, Emil L, et. all. &amp;quot;Bovine Liver Glutamate Dehydrogenase: Tentative Amino Acid Sequence; Identification of a Reactive Lysine; Nitration of a Specific Tyrosine and Loss of Allosteric Inhibition by Guanosine Triphosphate.&amp;quot; Proceedings of the National Academy of Sciences 67.2 (1970): 724-730. Print.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620221</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620221"/>
		<updated>2012-11-28T20:42:43Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, endoglucanase is mostly found in the form of a complex that is made up of three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. A loop of the protein chain forms a tunnel that encloses the active site. This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The figure on the right shows the two domains of GDH.  The orange represent the glutamate binding sites and the blue sites represent the domain involved in assembly of the hexamer.&lt;br /&gt;
&amp;lt;scene name=&#039;Sandbox_Reserved_655/Domains/1&#039;&amp;gt;Domain&amp;lt;/scene&amp;gt;&lt;br /&gt;
 &lt;br /&gt;
[[Image:structure.jpeg]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
NH4+  +  α-ketoglutarate  + NADPH  +  2 H+ → glutamate +  NADP+   +  H2O&lt;br /&gt;
::[[Image:glutamatedehydrogenase.jpeg]]&lt;br /&gt;
&lt;br /&gt;
Glutamate dehydrogenase is important in nitrogen and glutamate metabolism and energy homeostasis. In the reaction above the forward reaction is essential in converting free ammonia and α-ketoglutarate to glutamate, an amino acid that is used for protein synthesis. The reverse reaction is key reaction that links amino acid metabolism with the Tricarboxylic Acid cycle (TCA cycle). Both reactions utilize nicotinamide nucleotide cofactors: NAD+ when nitrogen is released and NADPH when nitrogen is used. Glutamate dehydrogenase is regulated by cell energy charge.  This requires Adenosine triphosphate (ATP) and Guanosine triphosphate (GTP) are positive allosteric effectors for the forward reaction and Adenosine diphosphate (ADP) and Guanosine diphosphate are positive allosteric effectors for the reverse reaction. When the level of ATP is high, conversion of glutamate to α-ketoglurate and other TCA cycle intermediates is limited; when the cellular energy charge is low, glutamate is converted to ammonia and oxidizable TCA cycle intermediates. Glutamate is an important amino acid since it gives an amine group for many transamination reactions, thus, glutamate dehydrogenase is essential in producing this amino acid. (9)&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) F.D. Schubot, I.A. Kataeva, J. Chang, A.K. Shah, L.G. Ljungdahl, J.P. Rose, B.-C. Wang. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43 (2004), pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) G. Parsiegla, C. Reverbel, C. Tardif, H. Driguez, R. Haser. Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action&lt;br /&gt;
J. Mol. Biol., 375 (2008), pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Smith, Thomas J., and Peter E. Peterson. &amp;quot;The Structure of Bovine Glutamate Dehydrogenase Provides Insights into the Mechanism of Allostery.&amp;quot; Structure 7.7 (1999): 769-782. Print.&lt;br /&gt;
&lt;br /&gt;
(5) Smith, Emil L, et. all. &amp;quot;Bovine Liver Glutamate Dehydrogenase: Tentative Amino Acid Sequence; Identification of a Reactive Lysine; Nitration of a Specific Tyrosine and Loss of Allosteric Inhibition by Guanosine Triphosphate.&amp;quot; Proceedings of the National Academy of Sciences 67.2 (1970): 724-730. Print.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=File:3vdh_bio_r_500.jpg&amp;diff=1620219</id>
		<title>File:3vdh bio r 500.jpg</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=File:3vdh_bio_r_500.jpg&amp;diff=1620219"/>
		<updated>2012-11-28T19:53:36Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: uploaded a new version of &amp;quot;Image:3vdh bio r 500.jpg&amp;quot;&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=File:3vdh_bio_r_500.jpg&amp;diff=1620218</id>
		<title>File:3vdh bio r 500.jpg</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=File:3vdh_bio_r_500.jpg&amp;diff=1620218"/>
		<updated>2012-11-28T19:46:20Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: uploaded a new version of &amp;quot;Image:3vdh bio r 500.jpg&amp;quot;&lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=File:3vdh_bio_r_500.jpg&amp;diff=1620217</id>
		<title>File:3vdh bio r 500.jpg</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=File:3vdh_bio_r_500.jpg&amp;diff=1620217"/>
		<updated>2012-11-28T19:45:27Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620216</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620216"/>
		<updated>2012-11-28T19:36:05Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;1GLH&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, endoglucanase is mostly found in the form of a complex that is made up of three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. A loop of the protein chain forms a tunnel that encloses the active site. This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The figure on the right shows the two domains of GDH.  The orange represent the glutamate binding sites and the blue sites represent the domain involved in assembly of the hexamer.&lt;br /&gt;
&amp;lt;scene name=&#039;Sandbox_Reserved_655/Domains/1&#039;&amp;gt;Domain&amp;lt;/scene&amp;gt;&lt;br /&gt;
 &lt;br /&gt;
[[Image:structure.jpeg]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
NH4+  +  α-ketoglutarate  + NADPH  +  2 H+ → glutamate +  NADP+   +  H2O&lt;br /&gt;
::[[Image:glutamatedehydrogenase.jpeg]]&lt;br /&gt;
&lt;br /&gt;
Glutamate dehydrogenase is important in nitrogen and glutamate metabolism and energy homeostasis. In the reaction above the forward reaction is essential in converting free ammonia and α-ketoglutarate to glutamate, an amino acid that is used for protein synthesis. The reverse reaction is key reaction that links amino acid metabolism with the Tricarboxylic Acid cycle (TCA cycle). Both reactions utilize nicotinamide nucleotide cofactors: NAD+ when nitrogen is released and NADPH when nitrogen is used. Glutamate dehydrogenase is regulated by cell energy charge.  This requires Adenosine triphosphate (ATP) and Guanosine triphosphate (GTP) are positive allosteric effectors for the forward reaction and Adenosine diphosphate (ADP) and Guanosine diphosphate are positive allosteric effectors for the reverse reaction. When the level of ATP is high, conversion of glutamate to α-ketoglurate and other TCA cycle intermediates is limited; when the cellular energy charge is low, glutamate is converted to ammonia and oxidizable TCA cycle intermediates. Glutamate is an important amino acid since it gives an amine group for many transamination reactions, thus, glutamate dehydrogenase is essential in producing this amino acid. (9)&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) F.D. Schubot, I.A. Kataeva, J. Chang, A.K. Shah, L.G. Ljungdahl, J.P. Rose, B.-C. Wang. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43 (2004), pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) G. Parsiegla, C. Reverbel, C. Tardif, H. Driguez, R. Haser. Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action&lt;br /&gt;
J. Mol. Biol., 375 (2008), pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Smith, Thomas J., and Peter E. Peterson. &amp;quot;The Structure of Bovine Glutamate Dehydrogenase Provides Insights into the Mechanism of Allostery.&amp;quot; Structure 7.7 (1999): 769-782. Print.&lt;br /&gt;
&lt;br /&gt;
(5) Smith, Emil L, et. all. &amp;quot;Bovine Liver Glutamate Dehydrogenase: Tentative Amino Acid Sequence; Identification of a Reactive Lysine; Nitration of a Specific Tyrosine and Loss of Allosteric Inhibition by Guanosine Triphosphate.&amp;quot; Proceedings of the National Academy of Sciences 67.2 (1970): 724-730. Print.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620215</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620215"/>
		<updated>2012-11-28T19:28:16Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&lt;br /&gt;
{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;http://www.rcsb.org/pdb/images/3vdh_bio_r_500.jpg?bioNum=1&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, endoglucanase is mostly found in the form of a complex that is made up of three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. A loop of the protein chain forms a tunnel that encloses the active site. This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The figure on the right shows the two domains of GDH.  The orange represent the glutamate binding sites and the blue sites represent the domain involved in assembly of the hexamer.&lt;br /&gt;
&amp;lt;scene name=&#039;Sandbox_Reserved_655/Domains/1&#039;&amp;gt;Domain&amp;lt;/scene&amp;gt;&lt;br /&gt;
 &lt;br /&gt;
[[Image:structure.jpeg]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
NH4+  +  α-ketoglutarate  + NADPH  +  2 H+ → glutamate +  NADP+   +  H2O&lt;br /&gt;
::[[Image:glutamatedehydrogenase.jpeg]]&lt;br /&gt;
&lt;br /&gt;
Glutamate dehydrogenase is important in nitrogen and glutamate metabolism and energy homeostasis. In the reaction above the forward reaction is essential in converting free ammonia and α-ketoglutarate to glutamate, an amino acid that is used for protein synthesis. The reverse reaction is key reaction that links amino acid metabolism with the Tricarboxylic Acid cycle (TCA cycle). Both reactions utilize nicotinamide nucleotide cofactors: NAD+ when nitrogen is released and NADPH when nitrogen is used. Glutamate dehydrogenase is regulated by cell energy charge.  This requires Adenosine triphosphate (ATP) and Guanosine triphosphate (GTP) are positive allosteric effectors for the forward reaction and Adenosine diphosphate (ADP) and Guanosine diphosphate are positive allosteric effectors for the reverse reaction. When the level of ATP is high, conversion of glutamate to α-ketoglurate and other TCA cycle intermediates is limited; when the cellular energy charge is low, glutamate is converted to ammonia and oxidizable TCA cycle intermediates. Glutamate is an important amino acid since it gives an amine group for many transamination reactions, thus, glutamate dehydrogenase is essential in producing this amino acid. (9)&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) F.D. Schubot, I.A. Kataeva, J. Chang, A.K. Shah, L.G. Ljungdahl, J.P. Rose, B.-C. Wang. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43 (2004), pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) G. Parsiegla, C. Reverbel, C. Tardif, H. Driguez, R. Haser. Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action&lt;br /&gt;
J. Mol. Biol., 375 (2008), pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Smith, Thomas J., and Peter E. Peterson. &amp;quot;The Structure of Bovine Glutamate Dehydrogenase Provides Insights into the Mechanism of Allostery.&amp;quot; Structure 7.7 (1999): 769-782. Print.&lt;br /&gt;
&lt;br /&gt;
(5) Smith, Emil L, et. all. &amp;quot;Bovine Liver Glutamate Dehydrogenase: Tentative Amino Acid Sequence; Identification of a Reactive Lysine; Nitration of a Specific Tyrosine and Loss of Allosteric Inhibition by Guanosine Triphosphate.&amp;quot; Proceedings of the National Academy of Sciences 67.2 (1970): 724-730. Print.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620213</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620213"/>
		<updated>2012-11-28T19:20:16Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;Structure load=&#039;3VDH&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Insert caption here&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&amp;lt;!-- PLEASE DO NOT DELETE THIS TEMPLATE --&amp;gt;&lt;br /&gt;
{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, endoglucanase is mostly found in the form of a complex that is made up of three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. A loop of the protein chain forms a tunnel that encloses the active site. This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The figure on the right shows the two domains of GDH.  The orange represent the glutamate binding sites and the blue sites represent the domain involved in assembly of the hexamer.&lt;br /&gt;
&amp;lt;scene name=&#039;Sandbox_Reserved_655/Domains/1&#039;&amp;gt;Domain&amp;lt;/scene&amp;gt;&lt;br /&gt;
 &lt;br /&gt;
[[Image:structure.jpeg]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
NH4+  +  α-ketoglutarate  + NADPH  +  2 H+ → glutamate +  NADP+   +  H2O&lt;br /&gt;
::[[Image:glutamatedehydrogenase.jpeg]]&lt;br /&gt;
&lt;br /&gt;
Glutamate dehydrogenase is important in nitrogen and glutamate metabolism and energy homeostasis. In the reaction above the forward reaction is essential in converting free ammonia and α-ketoglutarate to glutamate, an amino acid that is used for protein synthesis. The reverse reaction is key reaction that links amino acid metabolism with the Tricarboxylic Acid cycle (TCA cycle). Both reactions utilize nicotinamide nucleotide cofactors: NAD+ when nitrogen is released and NADPH when nitrogen is used. Glutamate dehydrogenase is regulated by cell energy charge.  This requires Adenosine triphosphate (ATP) and Guanosine triphosphate (GTP) are positive allosteric effectors for the forward reaction and Adenosine diphosphate (ADP) and Guanosine diphosphate are positive allosteric effectors for the reverse reaction. When the level of ATP is high, conversion of glutamate to α-ketoglurate and other TCA cycle intermediates is limited; when the cellular energy charge is low, glutamate is converted to ammonia and oxidizable TCA cycle intermediates. Glutamate is an important amino acid since it gives an amine group for many transamination reactions, thus, glutamate dehydrogenase is essential in producing this amino acid. (9)&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) F.D. Schubot, I.A. Kataeva, J. Chang, A.K. Shah, L.G. Ljungdahl, J.P. Rose, B.-C. Wang. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43 (2004), pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) G. Parsiegla, C. Reverbel, C. Tardif, H. Driguez, R. Haser. Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action&lt;br /&gt;
J. Mol. Biol., 375 (2008), pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Smith, Thomas J., and Peter E. Peterson. &amp;quot;The Structure of Bovine Glutamate Dehydrogenase Provides Insights into the Mechanism of Allostery.&amp;quot; Structure 7.7 (1999): 769-782. Print.&lt;br /&gt;
&lt;br /&gt;
(5) Smith, Emil L, et. all. &amp;quot;Bovine Liver Glutamate Dehydrogenase: Tentative Amino Acid Sequence; Identification of a Reactive Lysine; Nitration of a Specific Tyrosine and Loss of Allosteric Inhibition by Guanosine Triphosphate.&amp;quot; Proceedings of the National Academy of Sciences 67.2 (1970): 724-730. Print.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620212</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1620212"/>
		<updated>2012-11-28T19:10:14Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!-- PLEASE DO NOT DELETE THIS TEMPLATE --&amp;gt;&lt;br /&gt;
{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;3vdh&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process. Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes, produced chiefly by fungi, bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain (Kumar et al., 2008). &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, endoglucanase is mostly found in the form of a complex that is made up of three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. A loop of the protein chain forms a tunnel that encloses the active site. This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
The figure on the right shows the two domains of GDH.  The orange represent the glutamate binding sites and the blue sites represent the domain involved in assembly of the hexamer.&lt;br /&gt;
&amp;lt;scene name=&#039;Sandbox_Reserved_655/Domains/1&#039;&amp;gt;Domain&amp;lt;/scene&amp;gt;&lt;br /&gt;
 &lt;br /&gt;
[[Image:structure.jpeg]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
NH4+  +  α-ketoglutarate  + NADPH  +  2 H+ → glutamate +  NADP+   +  H2O&lt;br /&gt;
::[[Image:glutamatedehydrogenase.jpeg]]&lt;br /&gt;
&lt;br /&gt;
Glutamate dehydrogenase is important in nitrogen and glutamate metabolism and energy homeostasis. In the reaction above the forward reaction is essential in converting free ammonia and α-ketoglutarate to glutamate, an amino acid that is used for protein synthesis. The reverse reaction is key reaction that links amino acid metabolism with the Tricarboxylic Acid cycle (TCA cycle). Both reactions utilize nicotinamide nucleotide cofactors: NAD+ when nitrogen is released and NADPH when nitrogen is used. Glutamate dehydrogenase is regulated by cell energy charge.  This requires Adenosine triphosphate (ATP) and Guanosine triphosphate (GTP) are positive allosteric effectors for the forward reaction and Adenosine diphosphate (ADP) and Guanosine diphosphate are positive allosteric effectors for the reverse reaction. When the level of ATP is high, conversion of glutamate to α-ketoglurate and other TCA cycle intermediates is limited; when the cellular energy charge is low, glutamate is converted to ammonia and oxidizable TCA cycle intermediates. Glutamate is an important amino acid since it gives an amine group for many transamination reactions, thus, glutamate dehydrogenase is essential in producing this amino acid. (9)&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) F.D. Schubot, I.A. Kataeva, J. Chang, A.K. Shah, L.G. Ljungdahl, J.P. Rose, B.-C. Wang. Structural basis for the exocellulase activity of the cellobiohydrolase CbhA from Clostridium thermocellum Biochemistry, 43 (2004), pp. 1163–1170&lt;br /&gt;
&lt;br /&gt;
(2) G. Parsiegla, C. Reverbel, C. Tardif, H. Driguez, R. Haser. Structures of mutants of cellulase Cel48F of Clostridium cellulotyticum in complex with long hemithiocellooligosaccharides give rise to a new view of the substrate pathway during processive action&lt;br /&gt;
J. Mol. Biol., 375 (2008), pp. 499–510&lt;br /&gt;
&lt;br /&gt;
(3) Kumar, R., Sing, S., Singh, O.V. 2008. Bioconversion of lignocellulosic biomass: biochemical and molecular perspectives. J Ind Microbiol Biotechnol. 35: 377-391.&lt;br /&gt;
&lt;br /&gt;
(4) Smith, Thomas J., and Peter E. Peterson. &amp;quot;The Structure of Bovine Glutamate Dehydrogenase Provides Insights into the Mechanism of Allostery.&amp;quot; Structure 7.7 (1999): 769-782. Print.&lt;br /&gt;
&lt;br /&gt;
(5) Smith, Emil L, et. all. &amp;quot;Bovine Liver Glutamate Dehydrogenase: Tentative Amino Acid Sequence; Identification of a Reactive Lysine; Nitration of a Specific Tyrosine and Loss of Allosteric Inhibition by Guanosine Triphosphate.&amp;quot; Proceedings of the National Academy of Sciences 67.2 (1970): 724-730. Print.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1616422</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1616422"/>
		<updated>2012-11-28T13:08:15Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!-- PLEASE DO NOT DELETE THIS TEMPLATE --&amp;gt;&lt;br /&gt;
{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;1clc&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Cellulases are enzymes that catalyze the hydrolysis of cellulose and belong to a group of enzymes termed glycoside hydrolases (GHs). Several members of the GH family demonstrate a modular architecture composed of one or two catalytic modules connected to several kinds of accessory modules (Schubot et al., 2004). The accessory modules can be involved in numerous functions. For example, some cellulases contain carbohydrate-binding modules (CBMs), which enhance the association of the catalytic modules with insoluble carbohydrates. Cellulases have been characterized as endo or exo according to their mode of action on the substrate (Parsiegla et al., 2002). The endocellulases cleave the cellulose chain at arbitrary points, while exocellulases cleave at the terminus of a chain to start the degradation process.Beta-1,4-glycosidic bonds link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes produced chiefly by fungi; bacteria and protozoans, specifically cleave the internal bonds of the cellulose chain. &lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, endoglucanase is mostly found in the form of a complex that is made up of three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. A loop of the protein chain forms a tunnel that encloses the active site. This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007).&lt;br /&gt;
&lt;br /&gt;
Glutamate Dehydrogenase is a hexamer that is comprised of two trimer subunits.  These two subunits are stacked on top of each other and composed of three domains.  The top of each domain contains a &amp;quot;NAD-binding domain&amp;quot; that has the conserved nucleotide-binding motif.  A larger helix-loop-helix structure rises above this and is referred to as an &amp;quot;antenna.&amp;quot;  This antenna contains approximately 50 amino acids and is thought to play a major role in regulation of the enzyme.  This antennae structure is only found in animals. (1)  The bottom domain contacts a domain in the other trimer, holding the two trimers together.  The total size of each of the subunits is approximately 56.1 kD and 506 amino acids long. (5)&lt;br /&gt;
&lt;br /&gt;
When a substrate binds to the enzyme it binds to the deep recess of the cleft between the NAD binding domain and the lower domain.  Along the outside surface of the cleft a coenzyme (NAD+) binds to the C-terminal end causing the binding domain to rotate by about 18 degrees and close down on the substrate and coenzyme. (2)  The active sites for GDH are located at residues around 182-187.  &amp;lt;scene name=&#039;Sandbox_Reserved_641/Active_sites/1&#039;&amp;gt;Active Sites&amp;lt;/scene&amp;gt;  Residues at the locations of 200-206, 375-370, and 421-423 are involved in closing the cleft between the domains.   As the cleft is closing the antenna pushes against the pivot helix of the adjacent subunit.  The pivot helix rotates counter clockwise around both the helical axis and the trimer 3-fold axis.  The hexamer then compresses the inner core showing that catalysis involves the entire hexamer. (8)&lt;br /&gt;
&lt;br /&gt;
The figure on the right shows the two domains of GDH.  The orange represent the glutamate binding sites and the blue sites represent the domain involved in assembly of the hexamer.&lt;br /&gt;
&amp;lt;scene name=&#039;Sandbox_Reserved_641/Domains/1&#039;&amp;gt;Domain&amp;lt;/scene&amp;gt;&lt;br /&gt;
 &lt;br /&gt;
[[Image:structure.jpeg]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
NH4+  +  α-ketoglutarate  + NADPH  +  2 H+ → glutamate +  NADP+   +  H2O&lt;br /&gt;
::[[Image:glutamatedehydrogenase.jpeg]]&lt;br /&gt;
&lt;br /&gt;
Glutamate dehydrogenase is important in nitrogen and glutamate metabolism and energy homeostasis. In the reaction above the forward reaction is essential in converting free ammonia and α-ketoglutarate to glutamate, an amino acid that is used for protein synthesis. The reverse reaction is key reaction that links amino acid metabolism with the Tricarboxylic Acid cycle (TCA cycle). Both reactions utilize nicotinamide nucleotide cofactors: NAD+ when nitrogen is released and NADPH when nitrogen is used. Glutamate dehydrogenase is regulated by cell energy charge.  This requires Adenosine triphosphate (ATP) and Guanosine triphosphate (GTP) are positive allosteric effectors for the forward reaction and Adenosine diphosphate (ADP) and Guanosine diphosphate are positive allosteric effectors for the reverse reaction. When the level of ATP is high, conversion of glutamate to α-ketoglurate and other TCA cycle intermediates is limited; when the cellular energy charge is low, glutamate is converted to ammonia and oxidizable TCA cycle intermediates. Glutamate is an important amino acid since it gives an amine group for many transamination reactions, thus, glutamate dehydrogenase is essential in producing this amino acid. (9)&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) Smith, Thomas J., and Charles A. Stanley. &amp;quot;Untangling the Glutamate Dehydrogenase Allosteric Nightmare.&amp;quot; Trends in Biochemical Science 33.11 (2008): 557-564. Print.&lt;br /&gt;
&lt;br /&gt;
(2) Franco, Ann. &amp;quot;Reaction Mechanism of L-Glutamate Dehydrogenase.&amp;quot; European Journal of Biochemistry 45(1974): 407-424. Print.&lt;br /&gt;
&lt;br /&gt;
(3) Baker, Patrick J, et. all. &amp;quot;Subunit Assembly and Active Site Location in the Structure of Glutamate Dehydrogenase.&amp;quot; Proteins: Structure, Function and Genetrics 12(1992): 75-86. Print.&lt;br /&gt;
&lt;br /&gt;
(4) Smith, Thomas J., and Peter E. Peterson. &amp;quot;The Structure of Bovine Glutamate Dehydrogenase Provides Insights into the Mechanism of Allostery.&amp;quot; Structure 7.7 (1999): 769-782. Print.&lt;br /&gt;
&lt;br /&gt;
(5) Smith, Emil L, et. all. &amp;quot;Bovine Liver Glutamate Dehydrogenase: Tentative Amino Acid Sequence; Identification of a Reactive Lysine; Nitration of a Specific Tyrosine and Loss of Allosteric Inhibition by Guanosine Triphosphate.&amp;quot; Proceedings of the National Academy of Sciences 67.2 (1970): 724-730. Print.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1609488</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1609488"/>
		<updated>2012-11-18T22:30:26Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!-- PLEASE DO NOT DELETE THIS TEMPLATE --&amp;gt;&lt;br /&gt;
{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;1clc&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Beta-1,4-Endoglucanase is a specific enzyme that catalyzes the hydrolysis of cellulose. It is produced chiefly by fungi, bacteria, and protozoans. Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Beta-1,4-glycosidic bonds (hence the name, beta-1,4-endoglucanase) link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes specifically cleave the internal bonds of the cellulose chain.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, endoglucanase is mostly found in the form of a complex that is made up of three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. A loop of the protein chain forms a tunnel that encloses the active site. This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007)&lt;br /&gt;
&lt;br /&gt;
Today, one of the primary research uses for glutamate dehydrogenase is to determine how well the human liver is functioning.  If the level of GDH is too high that could indicate necrosis of the liver. (7)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate Dehydrogenase is a hexamer that is comprised of two trimer subunits.  These two subunits are stacked on top of each other and composed of three domains.  The top of each domain contains a &amp;quot;NAD-binding domain&amp;quot; that has the conserved nucleotide-binding motif.  A larger helix-loop-helix structure rises above this and is referred to as an &amp;quot;antenna.&amp;quot;  This antenna contains approximately 50 amino acids and is thought to play a major role in regulation of the enzyme.  This antennae structure is only found in animals. (1)  The bottom domain contacts a domain in the other trimer, holding the two trimers together.  The total size of each of the subunits is approximately 56.1 kD and 506 amino acids long. (5)&lt;br /&gt;
&lt;br /&gt;
When a substrate binds to the enzyme it binds to the deep recess of the cleft between the NAD binding domain and the lower domain.  Along the outside surface of the cleft a coenzyme (NAD+) binds to the C-terminal end causing the binding domain to rotate by about 18 degrees and close down on the substrate and coenzyme. (2)  The active sites for GDH are located at residues around 182-187.  &amp;lt;scene name=&#039;Sandbox_Reserved_641/Active_sites/1&#039;&amp;gt;Active Sites&amp;lt;/scene&amp;gt;  Residues at the locations of 200-206, 375-370, and 421-423 are involved in closing the cleft between the domains.   As the cleft is closing the antenna pushes against the pivot helix of the adjacent subunit.  The pivot helix rotates counter clockwise around both the helical axis and the trimer 3-fold axis.  The hexamer then compresses the inner core showing that catalysis involves the entire hexamer. (8)&lt;br /&gt;
&lt;br /&gt;
The figure on the right shows the two domains of GDH.  The orange represent the glutamate binding sites and the blue sites represent the domain involved in assembly of the hexamer.&lt;br /&gt;
&amp;lt;scene name=&#039;Sandbox_Reserved_641/Domains/1&#039;&amp;gt;Domain&amp;lt;/scene&amp;gt;&lt;br /&gt;
 &lt;br /&gt;
[[Image:structure.jpeg]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
NH4+  +  α-ketoglutarate  + NADPH  +  2 H+ → glutamate +  NADP+   +  H2O&lt;br /&gt;
::[[Image:glutamatedehydrogenase.jpeg]]&lt;br /&gt;
&lt;br /&gt;
Glutamate dehydrogenase is important in nitrogen and glutamate metabolism and energy homeostasis. In the reaction above the forward reaction is essential in converting free ammonia and α-ketoglutarate to glutamate, an amino acid that is used for protein synthesis. The reverse reaction is key reaction that links amino acid metabolism with the Tricarboxylic Acid cycle (TCA cycle). Both reactions utilize nicotinamide nucleotide cofactors: NAD+ when nitrogen is released and NADPH when nitrogen is used. Glutamate dehydrogenase is regulated by cell energy charge.  This requires Adenosine triphosphate (ATP) and Guanosine triphosphate (GTP) are positive allosteric effectors for the forward reaction and Adenosine diphosphate (ADP) and Guanosine diphosphate are positive allosteric effectors for the reverse reaction. When the level of ATP is high, conversion of glutamate to α-ketoglurate and other TCA cycle intermediates is limited; when the cellular energy charge is low, glutamate is converted to ammonia and oxidizable TCA cycle intermediates. Glutamate is an important amino acid since it gives an amine group for many transamination reactions, thus, glutamate dehydrogenase is essential in producing this amino acid. (9)&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) Smith, Thomas J., and Charles A. Stanley. &amp;quot;Untangling the Glutamate Dehydrogenase Allosteric Nightmare.&amp;quot; Trends in Biochemical Science 33.11 (2008): 557-564. Print.&lt;br /&gt;
&lt;br /&gt;
(2) Franco, Ann. &amp;quot;Reaction Mechanism of L-Glutamate Dehydrogenase.&amp;quot; European Journal of Biochemistry 45(1974): 407-424. Print.&lt;br /&gt;
&lt;br /&gt;
(3) Baker, Patrick J, et. all. &amp;quot;Subunit Assembly and Active Site Location in the Structure of Glutamate Dehydrogenase.&amp;quot; Proteins: Structure, Function and Genetrics 12(1992): 75-86. Print.&lt;br /&gt;
&lt;br /&gt;
(4) Smith, Thomas J., and Peter E. Peterson. &amp;quot;The Structure of Bovine Glutamate Dehydrogenase Provides Insights into the Mechanism of Allostery.&amp;quot; Structure 7.7 (1999): 769-782. Print.&lt;br /&gt;
&lt;br /&gt;
(5) Smith, Emil L, et. all. &amp;quot;Bovine Liver Glutamate Dehydrogenase: Tentative Amino Acid Sequence; Identification of a Reactive Lysine; Nitration of a Specific Tyrosine and Loss of Allosteric Inhibition by Guanosine Triphosphate.&amp;quot; Proceedings of the National Academy of Sciences 67.2 (1970): 724-730. Print.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1609487</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1609487"/>
		<updated>2012-11-18T22:21:16Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!-- PLEASE DO NOT DELETE THIS TEMPLATE --&amp;gt;&lt;br /&gt;
{{Sandbox_Reserved_Robert_B_Rose_2}}&lt;br /&gt;
&amp;lt;!-- PLEASE ADD YOUR CONTENT BELOW HERE --&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;6CEL&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Beta-1,4-Endoglucanase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Beta-1,4-Endoglucanase is a specific enzyme that catalyzes the hydrolysis of cellulose. It is produced chiefly by fungi, bacteria, and protozoans. Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Beta-1,4-glycosidic bonds (hence the name, beta-1,4-endoglucanase) link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes specifically cleave the internal bonds of the cellulose chain.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, endoglucanase is mostly found in the form of a complex that is made up of three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. A loop of the protein chain forms a tunnel that encloses the active site. This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007)&lt;br /&gt;
&lt;br /&gt;
Today, one of the primary research uses for glutamate dehydrogenase is to determine how well the human liver is functioning.  If the level of GDH is too high that could indicate necrosis of the liver. (7)&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate Dehydrogenase is a hexamer that is comprised of two trimer subunits.  These two subunits are stacked on top of each other and composed of three domains.  The top of each domain contains a &amp;quot;NAD-binding domain&amp;quot; that has the conserved nucleotide-binding motif.  A larger helix-loop-helix structure rises above this and is referred to as an &amp;quot;antenna.&amp;quot;  This antenna contains approximately 50 amino acids and is thought to play a major role in regulation of the enzyme.  This antennae structure is only found in animals. (1)  The bottom domain contacts a domain in the other trimer, holding the two trimers together.  The total size of each of the subunits is approximately 56.1 kD and 506 amino acids long. (5)&lt;br /&gt;
&lt;br /&gt;
When a substrate binds to the enzyme it binds to the deep recess of the cleft between the NAD binding domain and the lower domain.  Along the outside surface of the cleft a coenzyme (NAD+) binds to the C-terminal end causing the binding domain to rotate by about 18 degrees and close down on the substrate and coenzyme. (2)  The active sites for GDH are located at residues around 182-187.  &amp;lt;scene name=&#039;Sandbox_Reserved_641/Active_sites/1&#039;&amp;gt;Active Sites&amp;lt;/scene&amp;gt;  Residues at the locations of 200-206, 375-370, and 421-423 are involved in closing the cleft between the domains.   As the cleft is closing the antenna pushes against the pivot helix of the adjacent subunit.  The pivot helix rotates counter clockwise around both the helical axis and the trimer 3-fold axis.  The hexamer then compresses the inner core showing that catalysis involves the entire hexamer. (8)&lt;br /&gt;
&lt;br /&gt;
The figure on the right shows the two domains of GDH.  The orange represent the glutamate binding sites and the blue sites represent the domain involved in assembly of the hexamer.&lt;br /&gt;
&amp;lt;scene name=&#039;Sandbox_Reserved_641/Domains/1&#039;&amp;gt;Domain&amp;lt;/scene&amp;gt;&lt;br /&gt;
 &lt;br /&gt;
[[Image:structure.jpeg]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
NH4+  +  α-ketoglutarate  + NADPH  +  2 H+ → glutamate +  NADP+   +  H2O&lt;br /&gt;
::[[Image:glutamatedehydrogenase.jpeg]]&lt;br /&gt;
&lt;br /&gt;
Glutamate dehydrogenase is important in nitrogen and glutamate metabolism and energy homeostasis. In the reaction above the forward reaction is essential in converting free ammonia and α-ketoglutarate to glutamate, an amino acid that is used for protein synthesis. The reverse reaction is key reaction that links amino acid metabolism with the Tricarboxylic Acid cycle (TCA cycle). Both reactions utilize nicotinamide nucleotide cofactors: NAD+ when nitrogen is released and NADPH when nitrogen is used. Glutamate dehydrogenase is regulated by cell energy charge.  This requires Adenosine triphosphate (ATP) and Guanosine triphosphate (GTP) are positive allosteric effectors for the forward reaction and Adenosine diphosphate (ADP) and Guanosine diphosphate are positive allosteric effectors for the reverse reaction. When the level of ATP is high, conversion of glutamate to α-ketoglurate and other TCA cycle intermediates is limited; when the cellular energy charge is low, glutamate is converted to ammonia and oxidizable TCA cycle intermediates. Glutamate is an important amino acid since it gives an amine group for many transamination reactions, thus, glutamate dehydrogenase is essential in producing this amino acid. (9)&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) Smith, Thomas J., and Charles A. Stanley. &amp;quot;Untangling the Glutamate Dehydrogenase Allosteric Nightmare.&amp;quot; Trends in Biochemical Science 33.11 (2008): 557-564. Print.&lt;br /&gt;
&lt;br /&gt;
(2) Franco, Ann. &amp;quot;Reaction Mechanism of L-Glutamate Dehydrogenase.&amp;quot; European Journal of Biochemistry 45(1974): 407-424. Print.&lt;br /&gt;
&lt;br /&gt;
(3) Baker, Patrick J, et. all. &amp;quot;Subunit Assembly and Active Site Location in the Structure of Glutamate Dehydrogenase.&amp;quot; Proteins: Structure, Function and Genetrics 12(1992): 75-86. Print.&lt;br /&gt;
&lt;br /&gt;
(4) Smith, Thomas J., and Peter E. Peterson. &amp;quot;The Structure of Bovine Glutamate Dehydrogenase Provides Insights into the Mechanism of Allostery.&amp;quot; Structure 7.7 (1999): 769-782. Print.&lt;br /&gt;
&lt;br /&gt;
(5) Smith, Emil L, et. all. &amp;quot;Bovine Liver Glutamate Dehydrogenase: Tentative Amino Acid Sequence; Identification of a Reactive Lysine; Nitration of a Specific Tyrosine and Loss of Allosteric Inhibition by Guanosine Triphosphate.&amp;quot; Proceedings of the National Academy of Sciences 67.2 (1970): 724-730. Print.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1609486</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1609486"/>
		<updated>2012-11-18T21:55:51Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
&lt;hr /&gt;
&lt;div&gt;&amp;lt;!-- PLEASE DO NOT DELETE THIS TEMPLATE --&amp;gt;&lt;br /&gt;
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&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;Structure load=&#039;1V9L&#039; size=&#039;500&#039; frame=&#039;true&#039; align=&#039;right&#039; caption=&#039;Glutamate Dehydrogenase&#039; scene=&#039;Insert optional scene name here&#039; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Beta-1,4-Endoglucanase is a specific enzyme that catalyzes the hydrolysis of cellulose. It is produced chiefly by fungi, bacteria, and protozoans. Cellulose is one of the main components of the plant cell wall, found predominantly in the xylem tissue which is further protected by hemicellulose and pectin. Beta-1,4-glycosidic bonds (hence the name, beta-1,4-endoglucanase) link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes specifically cleave the internal bonds of the cellulose chain.&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
In the past 20 years, researchers have found that endoglucanases cannot break down polysaccharides efficiently without the help of non-catalytic carbohydrate-binding modules. Thus, endoglucanase is mostly found in the form of a complex that is made up of three separate domains. The main domain contains the large, globular catalytic domain which expresses the active site. A loop of the protein chain forms a tunnel that encloses the active site. This is attached at the O-glycosylated B block hinge region of the catalytic domain to the smaller, globular CBM at its C-terminal A block by a linker peptide made up of proline, serine, and threonine (Nimlos, et al., 2007)&lt;br /&gt;
&lt;br /&gt;
Today, one of the primary research uses for glutamate dehydrogenase is to determine how well the human liver is functioning.  If the level of GDH is too high that could indicate necrosis of the liver. (7)&lt;br /&gt;
-----&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Structure&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate Dehydrogenase is a hexamer that is comprised of two trimer subunits.  These two subunits are stacked on top of each other and composed of three domains.  The top of each domain contains a &amp;quot;NAD-binding domain&amp;quot; that has the conserved nucleotide-binding motif.  A larger helix-loop-helix structure rises above this and is referred to as an &amp;quot;antenna.&amp;quot;  This antenna contains approximately 50 amino acids and is thought to play a major role in regulation of the enzyme.  This antennae structure is only found in animals. (1)  The bottom domain contacts a domain in the other trimer, holding the two trimers together.  The total size of each of the subunits is approximately 56.1 kD and 506 amino acids long. (5)&lt;br /&gt;
&lt;br /&gt;
When a substrate binds to the enzyme it binds to the deep recess of the cleft between the NAD binding domain and the lower domain.  Along the outside surface of the cleft a coenzyme (NAD+) binds to the C-terminal end causing the binding domain to rotate by about 18 degrees and close down on the substrate and coenzyme. (2)  The active sites for GDH are located at residues around 182-187.  &amp;lt;scene name=&#039;Sandbox_Reserved_641/Active_sites/1&#039;&amp;gt;Active Sites&amp;lt;/scene&amp;gt;  Residues at the locations of 200-206, 375-370, and 421-423 are involved in closing the cleft between the domains.   As the cleft is closing the antenna pushes against the pivot helix of the adjacent subunit.  The pivot helix rotates counter clockwise around both the helical axis and the trimer 3-fold axis.  The hexamer then compresses the inner core showing that catalysis involves the entire hexamer. (8)&lt;br /&gt;
&lt;br /&gt;
The figure on the right shows the two domains of GDH.  The orange represent the glutamate binding sites and the blue sites represent the domain involved in assembly of the hexamer.&lt;br /&gt;
&amp;lt;scene name=&#039;Sandbox_Reserved_641/Domains/1&#039;&amp;gt;Domain&amp;lt;/scene&amp;gt;&lt;br /&gt;
 &lt;br /&gt;
[[Image:structure.jpeg]]&lt;br /&gt;
&lt;br /&gt;
&lt;br /&gt;
Methods for Purification:&lt;br /&gt;
Ammonium Sulfate Precipitation,&lt;br /&gt;
Ion Exchange Chromatography,&lt;br /&gt;
Affinity Chromatography on a column of allosteric inhibitor bound the Sepharose (6)&lt;br /&gt;
&lt;br /&gt;
Methods for Solving the Structure:&lt;br /&gt;
single-crystal X-ray-diffraction&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Mechanism&#039;&#039;&#039; ==&lt;br /&gt;
NH4+  +  α-ketoglutarate  + NADPH  +  2 H+ → glutamate +  NADP+   +  H2O&lt;br /&gt;
::[[Image:glutamatedehydrogenase.jpeg]]&lt;br /&gt;
&lt;br /&gt;
Glutamate dehydrogenase is important in nitrogen and glutamate metabolism and energy homeostasis. In the reaction above the forward reaction is essential in converting free ammonia and α-ketoglutarate to glutamate, an amino acid that is used for protein synthesis. The reverse reaction is key reaction that links amino acid metabolism with the Tricarboxylic Acid cycle (TCA cycle). Both reactions utilize nicotinamide nucleotide cofactors: NAD+ when nitrogen is released and NADPH when nitrogen is used. Glutamate dehydrogenase is regulated by cell energy charge.  This requires Adenosine triphosphate (ATP) and Guanosine triphosphate (GTP) are positive allosteric effectors for the forward reaction and Adenosine diphosphate (ADP) and Guanosine diphosphate are positive allosteric effectors for the reverse reaction. When the level of ATP is high, conversion of glutamate to α-ketoglurate and other TCA cycle intermediates is limited; when the cellular energy charge is low, glutamate is converted to ammonia and oxidizable TCA cycle intermediates. Glutamate is an important amino acid since it gives an amine group for many transamination reactions, thus, glutamate dehydrogenase is essential in producing this amino acid. (9)&lt;br /&gt;
&lt;br /&gt;
== &#039;&#039;&#039;Applications&#039;&#039;&#039; ==&lt;br /&gt;
Glutamate dehydrogenase is a mitochondrial enzyme present in the liver and can be used to determine how well the liver is functioning.  Blood serum levels are measured and if levels are high it could be indicative of hepatocellular necrosis. Liver diseases in which necrosis of heptocytes are involved, such as toxic liver damage hypoxic liver disease, are characterized by high serum GDH levels. GDH is important for distinguishing between acute viral hepatitis and acute toxic liver necrosis or acute hypoxic liver disease, particularly in the case of liver damage with very high aminotransferases. GDH is measure by conducting the following reaction. (7)&lt;br /&gt;
&lt;br /&gt;
::::::::GDH&lt;br /&gt;
a-oxoglutarate + NADH + NH4+ ---------------&amp;gt; glutamate + NAD+ +H2O&lt;br /&gt;
&lt;br /&gt;
As NADH is oxidized, the decrease in the absorbance per minute is measured spectrophotometrically at 340nm and is proportional to the GLDH activity.&lt;br /&gt;
&lt;br /&gt;
An example of this can be seen here: [https://docs.google.com/a/ncsu.edu/viewer?a=v&amp;amp;pid=gmail&amp;amp;attid=0.2&amp;amp;thid=13addc1ac3f18236&amp;amp;mt=application/pdf&amp;amp;url=https://mail.google.com/mail/u/0/?ui%3D2%26ik%3D5ad9b5051c%26view%3Datt%26th%3D13addc1ac3f18236%26attid%3D0.2%26disp%3Dsafe%26realattid%3Df_h998el621%26zw&amp;amp;sig=AHIEtbSNiAIgz_br1UY0dW534zXhAWFV4A]&lt;br /&gt;
&lt;br /&gt;
== Notes ==&lt;br /&gt;
&lt;br /&gt;
&amp;lt;references/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
(1) Smith, Thomas J., and Charles A. Stanley. &amp;quot;Untangling the Glutamate Dehydrogenase Allosteric Nightmare.&amp;quot; Trends in Biochemical Science 33.11 (2008): 557-564. Print.&lt;br /&gt;
&lt;br /&gt;
(2) Franco, Ann. &amp;quot;Reaction Mechanism of L-Glutamate Dehydrogenase.&amp;quot; European Journal of Biochemistry 45(1974): 407-424. Print.&lt;br /&gt;
&lt;br /&gt;
(3) Baker, Patrick J, et. all. &amp;quot;Subunit Assembly and Active Site Location in the Structure of Glutamate Dehydrogenase.&amp;quot; Proteins: Structure, Function and Genetrics 12(1992): 75-86. Print.&lt;br /&gt;
&lt;br /&gt;
(4) Smith, Thomas J., and Peter E. Peterson. &amp;quot;The Structure of Bovine Glutamate Dehydrogenase Provides Insights into the Mechanism of Allostery.&amp;quot; Structure 7.7 (1999): 769-782. Print.&lt;br /&gt;
&lt;br /&gt;
(5) Smith, Emil L, et. all. &amp;quot;Bovine Liver Glutamate Dehydrogenase: Tentative Amino Acid Sequence; Identification of a Reactive Lysine; Nitration of a Specific Tyrosine and Loss of Allosteric Inhibition by Guanosine Triphosphate.&amp;quot; Proceedings of the National Academy of Sciences 67.2 (1970): 724-730. Print.&lt;br /&gt;
&lt;br /&gt;
(6) Godinot, Catherine, et. all. &amp;quot;A Rapid and Efficient New Method of Purification of Glutamate Dehydrogenase by Affinity Chromatography on GTP-Sepharose.&amp;quot; Analytical Biochemistry 61.1 (1974): 264-270. Print.&lt;br /&gt;
&lt;br /&gt;
(7) Randox. &amp;quot;Glutamate Dehydrogenase (GLDH) for the Differential Diagnosis of Liver Disease.&amp;quot; (2007): N. pag. Print.&lt;br /&gt;
&lt;br /&gt;
(8) Minter, Mellisa. &amp;quot;Glutamate Dehydrogenase.&amp;quot; Oxidoreductases And The Reactions They Catalyze. University Of Wisconsin-Eau Claire, 2005. Web. 08 Nov. 2012. &amp;lt;http://www.chem.uwec.edu/Webpapers2005/mintermm/index.html&amp;gt;.&lt;br /&gt;
&lt;br /&gt;
(9) King, Michael. &amp;quot;Nitrogen Metabolism.&amp;quot; The Medical Biochemistry Page. Themedicalbiochemistrypage.org, 2012. Web. 08 Nov. 2012. &amp;lt;http://themedicalbiochemistrypage.org/nitrogen-metabolism.php&amp;gt;.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1609481</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1609481"/>
		<updated>2012-11-18T21:19:26Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
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&#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; &lt;br /&gt;
&lt;br /&gt;
Beta-1,4-Endoglucanase is a specific enzyme that catalyzes the hydrolysis of cellulose. It is produced chiefly by fungi, bacteria, and protozoans. Cellulose is one of the main components of the plant cell wall. The xylem tissue mainly consists of cellulose which is further protected by hemicellulose and pectin. Beta-1,4-glycosidic bonds (hence the name, beta-1,4-endoglucanase) link together the beta-D-glucopyranose units of cellulose. Beta-1-4-endoglucanase enzymes specifically cleave the internal bonds of the cellulose chain.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1605074</id>
		<title>Sandbox Reserved 655</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_655&amp;diff=1605074"/>
		<updated>2012-11-10T22:08:10Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
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&#039;&#039;&#039;Beta-1,4-Endoglucanase&#039;&#039;&#039; &lt;br /&gt;
&lt;br /&gt;
Beta-1,4-Endoglucanase is a specific enzyme that catalyzes the hydrolysis of cellulose. It is produced chiefly by fungi, bacteria, and protozoans.&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
	</entry>
	<entry>
		<id>https://proteopedia.org/index.php?title=Sandbox_Reserved_641&amp;diff=1543687</id>
		<title>Sandbox Reserved 641</title>
		<link rel="alternate" type="text/html" href="https://proteopedia.org/index.php?title=Sandbox_Reserved_641&amp;diff=1543687"/>
		<updated>2012-10-10T20:34:34Z</updated>

		<summary type="html">&lt;p&gt;Dami Adebambo: &lt;/p&gt;
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Dami&#039;s page&lt;/div&gt;</summary>
		<author><name>Dami Adebambo</name></author>
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