https://proteopedia.org/api.php?action=feedcontributions&feedformat=atom&user=Katelyn+BurkeProteopedia - User contributions [en]2026-10-02T18:00:17ZUser contributionsMediaWiki 1.43.8https://proteopedia.org/index.php?title=File:NrdH-NrdE_disulfide.png&diff=2398620File:NrdH-NrdE disulfide.png2015-04-26T19:24:18Z<p>Katelyn Burke: uploaded a new version of "Image:NrdH-NrdE disulfide.png": This mechanism shows the passing of electrons from NrdH to NrdE in the Ib Ribonucleotide Reduction Pathway.</p>
<hr />
<div>This mechanism shows the passing of electrons from NrdH to NrdE via disulfide bonds.</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2398619Sandbox Reserved 10612015-04-26T19:21:16Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='300' side='right' caption='Micobacterium tuberculosis NrdH' scene='69/694228/Mtnrdh/2'><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH (MtNrdH) is a small glutaredoxin-like protein involved in the electron transport chain in ribonucleotide reduction. Therefore, it is extremely important in DNA production and replication because it helps supply cells with deoxyribonucleotides. Reduction of MtNrdH results in the breaking of an internal disulfide bond at the active site, allowing it to accept electrons and pass them on downstream. Due to its imperative role in ribionucleotide reduction, MtNrdH is thought to be essential to the reproductive integrity of ''M. tuberculosis'', suggesting its role in infectivity and leading to its identification as a possible drug target.<ref name ="Swastik">Swastik, Phulera and Mande, Shekhar C. (2013) The Crystal Structure of Mycobacterium tuberculosis NrdH at 0.87Å Suggests a Possible Mode of Its Activity. Biochemistry 52, 4056-4065.</ref><br />
<br />
== Background ==<br />
<br />
[http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis'']resides in the lungs of a host. Upon becoming active, this bacterium results in a Tuberculosis infection (TB) and is the cause of symptoms such as chest pain, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013).<ref name="WHO">"Tuberculosis." Media Centre. World Health Organization, Web. 16 Mar. 2015. Media Centre. <http://www.who.int/mediacentre/factsheets/fs104/en/>.</ref> The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. TB is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative.<ref name="WHO" /><br />
<br />
<br />
== Structure == <br />
<br />
The <scene name='69/694228/Nrdh_structure/1'>MtNrdH structure</scene> determined by x-ray crystallography has 79 residues in a single polypeptide chain. The active site (shown in green) is dominated by a <scene name='69/694228/Nrdh_structure/3'>disulfide bond</scene> between Cys-11 and Cys-14, which serves as the site of reduction by thioredoxin reductase. <ref name="Swastik" /><br />
<br />
Many thioredoxin-like proteins have a similar active site region, which includes the <br />
<scene name='69/694228/Nrdh_structure/6'>thioredoxin fold</scene>, a large turn in the protein structure right before the disulfide bond. The residues directly following the fold, <scene name='69/694228/Nrdh_structure/5'>CVQC</scene>, are the most highly conserved of all areas of the protein across multiple species (Figure 1). <br />
[[Image:Weblogocvqc.png|thumb|center|upright=2.5|'''Figure 1.'''Weblogo diagram showing highly conserved CVQC region of NrdH in four separate protein structures from ''Nocardia seriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.<ref name="weblogo">Crooks GE, Hon G, Chandonia JM, Brenner SE WebLogo: A sequence logo generator,<br />
Genome Research, 14:1188-1190, (2004)</ref>]]<br />
<br />
==== Conformational Changes ====<br />
<br />
Exactly how this structure relates to function is somewhat debated, but it is hypothesized that the fold allows residues preceding the turn to interact with the CVQC region after the turn. A threonine-7 reside directly across the thioredoxin fold from the disulfide bond has been suggested to adopt two different conformations which differently affect the redox abilities of the protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/17'>"A" conformation</scene>, the alcohol oxygen of the threonine side chain (seen as a red ball) points towards the disulfide bond, forming an electrostatic interaction (represented by a short dashed line) between the two that prevents thioredoxin reductase (TrxR) from binding. Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/18'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space and enough electrostatic freedom for the ligand to bind and reduction to occur.<ref name="Swastik" /><br />
<br />
[[Image:Hydrophobic region 2.png|thumb|right| '''Figure 2.'''Hydrophobic region WSGFRP on the surface of MtNrdH (red) next to the active site (green.) Notice that this Hydrophobic region is heavily exposed to solvent. The WSGFRP sequence is thought to help thioredoxin reductase bind for reduction.<ref name="Swastik" /> <ref name="PyMol">The PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.</ref>]]<br />
<br />
The WSGFRP sequence, which is also highly conserved (Figure 3), is a nonpolar sequence that can be found on the surface of the molecule and is exposed to solvent (Figure 2). For this reason, it has been hypothesized that this sequence plays a role in the binding of thioredoxin reductase.<ref name="Swastik" /> Nonpolar residues on thioredoxin reductase would interact with the hydrophobic region, thus holding the thioredoxin reductase in place during reduction. <br />
<br />
<scene name='69/694227/Arg_68/4'>Arg-68</scene> is responsible for the stabilization of the hydrophobic region of NrdH. Arg-68 has two distinct conformations. In the <scene name='69/694227/Arg_68_conformation_1/4'>first conformation</scene>, Arg-68 is hydrogen bonded to His- 60 and Asp-59. When Arg-68 shifts to its <scene name='69/694227/Arg_68_conformation_2/5'>second conformation</scene>, it breaks its hydrogen bond with Asp-59. <ref name="Swastik" /> This reduction in hydrogen bonding gives the hydrophobic region more flexibility and is thought to occur when NrdH is in its inactive state. <br />
<br />
[[Image:Wsgfrpweblogo.png|thumb|center|upright=2.5|'''Figure 3.'''Weblogo diagram showing highly conserved WSGFRP region of NrdH in four separate protein structures from ''Nocardia seriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.<ref name="weblogo" />]]<br />
<br />
<br />
==== Stabilization ====<br />
The active site of the protein is stabilized through a <scene name='69/696879/Water_coordination/2'>hydrogen bond network</scene> involving the two highly conserved series of residues, CVQC (green) and WSGFRP (red). A water molecule appears to be a key part of the H-bonding network. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<ref name="Swastik" /><br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called [http://www.proteopedia.org/wiki/index.php/Ribonucleotide_reductase ribonucleotide reductase (RNR)] to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes.<ref name ="Kolberg">Kolberg, M., et al. (2004) Structure, function, and mechanism of ribonucleotide reductases. Biochim. Biophys. Acta 1699 (1−2), 1−34.</ref> Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). Ribonucleotide reductase utilizes free thiols to reduce NDP to dNDP. After both of the free thiols give up their electrons, they form a disulfide bond. To be able to perform another round of reduction, the disulfide bond needs to be reduced into free thiols again. In class Ia, RNR is reduced by either glutadoxin or thioredoxin, which also use disulfide bonds and free thiols to pass electrons.<ref>Nelson, David L., and Michael M. Cox. Lehninger Principles of Biochemistry. 5th ed. New York: W.H. Freeman, 2008. 888-889.</ref> In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH (Figure 4). Like thioredoxin and glutadoxin, NrdE and NrdH both use a disulfide reduction mechanism (Figure 5). Thioredoxin reductase uses NADPH to reduce NrdH <ref name="Makhlynets" />. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <ref name="Kolberg" /><br />
<br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|'''Figure 4.'''Ribonucleotide Reduction Class Ib general pathway.<ref name="Makhlynets">Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref> The role of NrdH is highlighted.]] <br />
<br />
[[Image:NrdH-NrdE disulfide.png|thumb|center|upright=2.5| '''Figure 5.''' The passing of electrons from NrdH to NrdE via disulfide reduction. <ref> Arne Holmgren, Thioredoxin structure and mechanism: conformational changes on oxidation of the active-site sulfhydryls to a disulfide, Structure, Volume 3, Issue 3, March 1995, Pages 239-243, ISSN 0969-2126, http://dx.doi.org/10.1016/S0969-2126(01)00153-8. </ref>.]]<br />
<br />
== Relevance ==<br />
<br />
Like most NrdHs, MtNrdH is similar in sequence to glutaredoxins, but structurally similar to thioredoxins (Figure 6). MtNrdH also accepts electrons from thioredoxin reductase, a characteristic of thioredoxins, but not glutaredoxins.<ref name="Swastik" /> [[Image:Image-Super imposed molecules.png|thumb|left|'''Figure 6.'''Structural comparison of NrdHs with "thioredoxin folds": ''E. Coli'' NrdH (green), ''C. ammoniagenes'' NrdH (blue), ''M. tuberculosis'' NrdH (red)<ref name="PyMol" />]] <br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', ''S. dysenteriae'', and ''C. glutamicium''<ref>Wang, M. et al. Mol Cell Proteomics 2012, doi:10.1074/mcp.O111.014704. http://pax-db.org/#!search?q=NrdH%250A</ref> <ref>Si, M.-R., Zhang, L., Yang, Z.-F., Xu, Y.-X., Liu, Y.-B., Jiang, C.-Y., … Liu, S.-J. (2014). NrdH Redoxin Enhances Resistance to Multiple Oxidative Stresses by Acting as a Peroxidase Cofactor in Corynebacterium glutamicum. Applied and Environmental Microbiology, 80(5), 1750–1762. doi:10.1128/AEM.03654-13</ref> In higher order multi-cellular organisms, however, the NrdH protein is replaced by more complex glutaredoxins or thioredoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. <ref name="Swastik" /> If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the [http://en.wikipedia.org/wiki/RNA_world RNA Wold Hypothesis], specifically describing the time frame of emergence of DNA based life. <br />
<br />
==Possible Drug Target==<br />
<br />
MtNrdH can serve as a potential drug target to treat tuberculosis. The genes encoding NrdE and NrdF2, a cofactor in class 1b ribonucleotide reduction, are essential for growth of M. tuberculosis in vitro.<ref>Mowa, M. B., et al. (2009) Function and regulation of class I ribonucleotide reductase-encoding genes in mycobacteria. J. Bacteriol. 191 (3), 985−995</ref> This suggests that M. tuberculosis relies solely on class Ib ribonucleotide reduction. If that is the case, NrdH may be an essential gene as well. Since NrdH is not found in humans, a drug that targets NrdH would be able to damage M. tuberculosis cells without hurting the human host. <br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2398614Sandbox Reserved 10612015-04-26T19:09:42Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='300' side='right' caption='Micobacterium tuberculosis NrdH' scene='69/694228/Mtnrdh/2'><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH (MtNrdH) is a small glutaredoxin-like protein involved in the electron transport chain in ribonucleotide reduction. Therefore, it is extremely important in DNA production and replication because it helps supply cells with deoxyribonucleotides. Reduction of MtNrdH results in the breaking of an internal disulfide bond at the active site, allowing it to accept electrons and pass them on downstream. Because of its imperative role in ribionucleotide reduction, MtNrdH is thought to be essential to the reproductive integrity of ''M. tuberculosis'', suggesting its role in infectivity and leading to its identification as a possible drug target.<ref name ="Swastik">Swastik, Phulera and Mande, Shekhar C. (2013) The Crystal Structure of Mycobacterium tuberculosis NrdH at 0.87Å Suggests a Possible Mode of Its Activity. Biochemistry 52, 4056-4065.</ref><br />
<br />
== Background ==<br />
<br />
[http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis'']resides in the lungs of a host and upon becoming active, results in a Tuberculosis infection (TB) and the ensuing symptoms of chest pain, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013).<ref name="WHO">"Tuberculosis." Media Centre. World Health Organization, Web. 16 Mar. 2015. Media Centre. <http://www.who.int/mediacentre/factsheets/fs104/en/>.</ref> The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. TB is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative.<ref name="WHO" /><br />
<br />
<br />
== Structure == <br />
<br />
The <scene name='69/694228/Nrdh_structure/1'>MtNrdH structure</scene> determined by x-ray crystallography has 79 residues in a single polypeptide chain. The active site (shown in green) is dominated by a <scene name='69/694228/Nrdh_structure/3'>disulfide bond</scene> between Cys-11 and Cys-14, which serves as the site of reduction by thioredoxin reductase. <ref name="Swastik" /><br />
<br />
Many thioredoxin-like proteins have a similar active site region, which includes the <br />
<scene name='69/694228/Nrdh_structure/6'>thioredoxin fold</scene>, a large turn in the protein structure right before the disulfide bond. The residues directly following the fold, <scene name='69/694228/Nrdh_structure/5'>CVQC</scene>, are the most highly conserved of all areas of the protein across multiple species (Figure 1). <br />
[[Image:Weblogocvqc.png|thumb|center|upright=2.5|'''Figure 1.'''Weblogo diagram showing highly conserved CVQC region of NrdH in four separate protein structures from ''Nocardia seriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.<ref name="weblogo">Crooks GE, Hon G, Chandonia JM, Brenner SE WebLogo: A sequence logo generator,<br />
Genome Research, 14:1188-1190, (2004)</ref>]]<br />
<br />
==== Conformational Changes ====<br />
<br />
Exactly how this structure relates to function is somewhat debated, but it is hypothesized that the fold allows residues preceding the turn to interact with the CVQC region after the turn. A threonine-7 reside directly across the thioredoxin fold from the disulfide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/17'>"A" conformation</scene>, the alcohol oxygen of the threonine side chain (seen as a red ball) points towards the disulfide bond, forming an electrostatic interaction (represented by a short dashed line) between the two that prevents thioredoxin reductase (TrxR) from binding. Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/18'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space and enough electrostatic freedom for the ligand to bind and reduction to occur.<ref name="Swastik" /><br />
<br />
[[Image:Hydrophobic region 2.png|thumb|right| '''Figure 2.'''Hydrophobic region WSGFRP on the surface of MtNrdH (red) next to the active site (green.) Notice that this Hydrophobic region is heavily exposed to solvent. This WSGFRP sequence is thought to help thioredoxin reductase bind for reduction.<ref name="Swastik" /> <ref name="PyMol">The PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.</ref>]]<br />
<br />
Another highly conserved series of residues is the WSGFRP sequence (Figure 3). This nonpolar sequence is found on the surface of the molecule and is exposed to solvent (Figure 2). For this reason, it has been hypothesized that this sequence plays a role in the binding of thioredoxin reductase. <ref name="Swastik" /><br />
<br />
<scene name='69/694227/Arg_68/4'>Arg-68</scene> is responsible for the stabilization of the hydrophobic region of NrdH. Arg-68 has two distinct conformations. In the <scene name='69/694227/Arg_68_conformation_1/4'>first conformation</scene>, Arg-68 is hydrogen bonded to His- 60 and Asp-59. When Arg-68 shifts to its <scene name='69/694227/Arg_68_conformation_2/5'>second conformation</scene>, it breaks its hydrogen bond with Asp-59. <ref name="Swastik" /> This reduction in hydrogen bonding gives the hydrophobic region more flexibility and is thought to occur when NrdH is in its inactive state. <br />
<br />
[[Image:Wsgfrpweblogo.png|thumb|center|upright=2.5|'''Figure 3.'''Weblogo diagram showing highly conserved WSGFRP region of NrdH in four separate protein structures from ''Nocardia seriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.<ref name="weblogo" />]]<br />
<br />
<br />
==== Stabilization ====<br />
The active site of the protein is stabilized through a <scene name='69/696879/Water_coordination/2'>hydrogen bond network</scene> involving the two highly conserved series of residues, CVQC (green) and WSGFRP (red). A water molecule appears to be a key part of the H-bonding network. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<ref name="Swastik" /><br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called [http://www.proteopedia.org/wiki/index.php/Ribonucleotide_reductase ribonucleotide reductase (RNR)] to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes.<ref name ="Kolberg">Kolberg, M., et al. (2004) Structure, function, and mechanism of ribonucleotide reductases. Biochim. Biophys. Acta 1699 (1−2), 1−34.</ref> Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). Ribonucleotide reductase utilizes free thiols to reduce NDP to dNDP. After both of the free thiols give up their electrons, they form a disulfide bond. To be able to perform another round of reduction, the disulfide bond needs to be reduced into free thiols again. In class Ia, RNR is reduced by either glutadoxin or thioredoxin, which also use disulfide bonds and free thiols to pass electrons.<ref>Nelson, David L., and Michael M. Cox. Lehninger Principles of Biochemistry. 5th ed. New York: W.H. Freeman, 2008. 888-889.</ref> In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH (Figure 4). Like thioredoxin and glutadoxin, NrdE and NrdH both use a disulfide reduction mechanism (Figure 5). Thioredoxin reductase uses NADPH to reduce NrdH <ref name="Makhlynets" />. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <ref name="Kolberg" /><br />
<br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|'''Figure 4.'''Ribonucleotide Reduction Class Ib general pathway.<ref name="Makhlynets">Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref> The role of NrdH is highlighted.]] <br />
<br />
[[Image:NrdH-NrdE disulfide.png|thumb|center|upright=2.5| '''Figure 5.''' The passing of electrons from NrdH to NrdE via disulfide reduction. <ref> Arne Holmgren, Thioredoxin structure and mechanism: conformational changes on oxidation of the active-site sulfhydryls to a disulfide, Structure, Volume 3, Issue 3, March 1995, Pages 239-243, ISSN 0969-2126, http://dx.doi.org/10.1016/S0969-2126(01)00153-8. </ref>.]]<br />
<br />
== Relevance ==<br />
<br />
Like most NrdHs, MtNrdH is similar in sequence to glutaredoxins, but structurally similar to thioredoxins (Figure 6). MtNrdH also accepts electrons from thioredoxin reductase, a characteristic of thioredoxins, but not glutaredoxins.<ref name="Swastik" /> [[Image:Image-Super imposed molecules.png|thumb|left|'''Figure 6.'''Structural comparison of NrdHs with "thioredoxin folds": ''E. Coli'' NrdH (green), ''C. ammoniagenes'' NrdH (blue), ''M. tuberculosis'' NrdH (red)<ref name="PyMol" />]] <br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', ''S. dysenteriae'', and ''C. glutamicium''<ref>Wang, M. et al. Mol Cell Proteomics 2012, doi:10.1074/mcp.O111.014704. http://pax-db.org/#!search?q=NrdH%250A</ref> <ref>Si, M.-R., Zhang, L., Yang, Z.-F., Xu, Y.-X., Liu, Y.-B., Jiang, C.-Y., … Liu, S.-J. (2014). NrdH Redoxin Enhances Resistance to Multiple Oxidative Stresses by Acting as a Peroxidase Cofactor in Corynebacterium glutamicum. Applied and Environmental Microbiology, 80(5), 1750–1762. doi:10.1128/AEM.03654-13</ref> In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or thioredoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. <ref name="Swastik" /> If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the [http://en.wikipedia.org/wiki/RNA_world RNA Wold Hypothesis], specifically describing the time frame of emergence of DNA based life. <br />
<br />
==Possible Drug Target==<br />
<br />
MtNrdH can serve as a potential drug target to treat tuberculosis. The genes encoding NrdE and NrdF2, a cofactor in class 1b ribonucleotide reduction, are essential for growth of M. tuberculosis in vitro.<ref>Mowa, M. B., et al. (2009) Function and regulation of class I ribonucleotide reductase-encoding genes in mycobacteria. J. Bacteriol. 191 (3), 985−995</ref> This suggests that M. tuberculosis relies solely on class Ib ribonucleotide reduction. If that is the case, NrdH may be an essential gene as well. Since NrdH is not found in humans, a drug that targets NrdH would be able to damage M. tuberculosis cells without hurting the human host.<br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2398613Sandbox Reserved 10612015-04-26T19:02:28Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='300' side='right' caption='Micobacterium tuberculosis NrdH' scene='69/694228/Mtnrdh/2'><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH (MtNrdH) is a small glutaredoxin-like protein involved in the electron transport chain in ribonucleotide reduction. Therefore, it is extremely important in DNA production and replication because it helps supply cells with deoxyribonucleotides. Reduction of MtNrdH results in the breaking of an internal disulfide bond at the active site, allowing it to accept electrons and pass them on downstream. Because of its imperative role in ribionucleotide reduction, MtNrdH is thought to be essential to the reproductive integrity of ''M. tuberculosis'', suggesting its role in infectivity and leading to its identification as a possible drug target.<ref name ="Swastik">Swastik, Phulera and Mande, Shekhar C. (2013) The Crystal Structure of Mycobacterium tuberculosis NrdH at 0.87Å Suggests a Possible Mode of Its Activity. Biochemistry 52, 4056-4065.</ref><br />
<br />
== Background ==<br />
<br />
[http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis'']resides in the lungs of a host and upon becoming active, results in a Tuberculosis infection (TB) and the ensuing symptoms of chest pain, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013).<ref name="WHO">"Tuberculosis." Media Centre. World Health Organization, Web. 16 Mar. 2015. Media Centre. <http://www.who.int/mediacentre/factsheets/fs104/en/>.</ref> The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. TB is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative.<ref name="WHO" /><br />
<br />
<br />
== Structure == <br />
<br />
The <scene name='69/694228/Nrdh_structure/1'>MtNrdH structure</scene> determined by x-ray crystallography has 79 residues in a single polypeptide chain. The active site (shown in green) is dominated by a <scene name='69/694228/Nrdh_structure/3'>disulfide bond</scene> between Cys-11 and Cys-14, which serves as the site of reduction by thioredoxin reductase. <ref name="Swastik" /><br />
<br />
Many thioredoxin-like proteins have a similar active site region, which includes the <br />
<scene name='69/694228/Nrdh_structure/6'>thioredoxin fold</scene>, a large turn in the protein structure right before the disulfide bond. The residues directly following the fold, <scene name='69/694228/Nrdh_structure/5'>CVQC</scene>, are the most highly conserved of all areas of the protein across multiple species (Figure 1). <br />
[[Image:Weblogocvqc.png|thumb|center|upright=2.5|'''Figure 1.'''Weblogo diagram showing highly conserved CVQC region of NrdH in four separate protein structures from ''Nocardia seriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.<ref name="weblogo">Crooks GE, Hon G, Chandonia JM, Brenner SE WebLogo: A sequence logo generator,<br />
Genome Research, 14:1188-1190, (2004)</ref>]]<br />
<br />
==== Conformational Changes ====<br />
<br />
Exactly how this structure relates to function is somewhat debated, but it is hypothesized that the fold allows residues preceding the turn to interact with the CVQC region after the turn. A threonine-7 reside directly across the thioredoxin fold from the disulfide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/17'>"A" conformation</scene>, the alcohol oxygen of the threonine side chain (seen as a red ball) points towards the disulfide bond, forming an electrostatic interaction (represented by a short dashed line) between the two that prevents thioredoxin reductase (TrxR) from binding. Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/18'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space and enough electrostatic freedom for the ligand to bind and reduction to occur.<ref name="Swastik" /><br />
<br />
[[Image:Hydrophobic region 2.png|thumb|right| '''Figure 2.'''Hydrophobic region WSGFRP on the surface of MtNrdH (red) next to the active site (green.) Notice that this Hydrophobic region is heavily exposed to solvent. This WSGFRP sequence is thought to help thioredoxin reductase bind for reduction.<ref name="Swastik" /> <ref name="PyMol">The PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.</ref>]]<br />
<br />
Another highly conserved series of residues is the WSGFRP sequence (Figure 3). This nonpolar sequence is found on the surface of the molecule and is exposed to solvent (Figure 2). For this reason, it has been hypothesized that this sequence plays a role in the binding of thioredoxin reductase. <ref name="Swastik" /><br />
<br />
<scene name='69/694227/Arg_68/4'>Arg-68</scene> is responsible for the stabilization of the hydrophobic region of NrdH. Arg-68 has two distinct conformations. In the <scene name='69/694227/Arg_68_conformation_1/4'>first conformation</scene>, Arg-68 is hydrogen bonded to His- 60 and Asp-59. When Arg-68 shifts to its <scene name='69/694227/Arg_68_conformation_2/5'>second conformation</scene>, it breaks its hydrogen bond with Asp-59. <ref name="Swastik" /> This reduction in hydrogen bonding gives the hydrophobic region more flexibility and is thought to occur when NrdH is in its inactive state. <br />
<br />
[[Image:Wsgfrpweblogo.png|thumb|center|upright=2.5|'''Figure 3.'''Weblogo diagram showing highly conserved WSGFRP region of NrdH in four separate protein structures from ''Nocardia seriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.<ref name="weblogo" />]]<br />
<br />
<br />
==== Stabilization ====<br />
The active site of the protein is stabilized through a <scene name='69/696879/Water_coordination/2'>hydrogen bond network</scene> involving the two highly conserved series of residues, CVQC (green) and WSGFRP (red). A water molecule appears to be a key part of the H-bonding network. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<ref name="Swastik" /><br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called [http://www.proteopedia.org/wiki/index.php/Ribonucleotide_reductase ribonucleotide reductase (RNR)] to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes.<ref name ="Kolberg">Kolberg, M., et al. (2004) Structure, function, and mechanism of ribonucleotide reductases. Biochim. Biophys. Acta 1699 (1−2), 1−34.</ref> Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). Ribonucleotide reductase utilizes free thiols to reduce NDP to dNDP. After both of the free thiols give up their electrons, they form a disulfide bond. To be able to perform another round of reduction, the disulfide bond needs to be reduced into free thiols again. In class Ia, RNR is reduced by either glutadoxin or thioredoxin, which are first reduced by glutadoxin reductase and thioredoxin reductase, respectively.<ref>Nelson, David L., and Michael M. Cox. Lehninger Principles of Biochemistry. 5th ed. New York: W.H. Freeman, 2008. 888-889.</ref> In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH (Figure 4). Like ribonucleotide reductase, NrdE and NrdH both use the making and breaking of disulfide bonds to pass electrons down the chain. Thioredoxin reductase uses NADPH to reduce NrdH <ref name="Makhlynets" />. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <ref name="Kolberg" /><br />
<br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|'''Figure 4.'''Ribonucleotide Reduction Class Ib general mechanism.<ref name="Makhlynets">Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref> The role of NrdH is highlighted.]] <br />
<br />
[[Image:]]<br />
<br />
== Relevance ==<br />
<br />
Like most NrdHs, MtNrdH is similar in sequence to glutaredoxins, but structurally similar to thioredoxins (Figure 6). MtNrdH also accepts electrons from thioredoxin reductase, a characteristic of thioredoxins, but not glutaredoxins.<ref name="Swastik" /> [[Image:Image-Super imposed molecules.png|thumb|left|'''Figure 6.'''Structural comparison of NrdHs with "thioredoxin folds": ''E. Coli'' NrdH (green), ''C. ammoniagenes'' NrdH (blue), ''M. tuberculosis'' NrdH (red)<ref name="PyMol" />]] <br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', ''S. dysenteriae'', and ''C. glutamicium''<ref>Wang, M. et al. Mol Cell Proteomics 2012, doi:10.1074/mcp.O111.014704. http://pax-db.org/#!search?q=NrdH%250A</ref> <ref>Si, M.-R., Zhang, L., Yang, Z.-F., Xu, Y.-X., Liu, Y.-B., Jiang, C.-Y., … Liu, S.-J. (2014). NrdH Redoxin Enhances Resistance to Multiple Oxidative Stresses by Acting as a Peroxidase Cofactor in Corynebacterium glutamicum. Applied and Environmental Microbiology, 80(5), 1750–1762. doi:10.1128/AEM.03654-13</ref> In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or thioredoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. <ref name="Swastik" /> If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the [http://en.wikipedia.org/wiki/RNA_world RNA Wold Hypothesis], specifically describing the time frame of emergence of DNA based life. <br />
<br />
==Possible Drug Target==<br />
<br />
MtNrdH can serve as a potential drug target to treat tuberculosis. The genes encoding NrdE and NrdF2, a cofactor in class 1b ribonucleotide reduction, are essential for growth of M. tuberculosis in vitro.<ref>Mowa, M. B., et al. (2009) Function and regulation of class I ribonucleotide reductase-encoding genes in mycobacteria. J. Bacteriol. 191 (3), 985−995</ref> This suggests that M. tuberculosis relies solely on class Ib ribonucleotide reduction. If that is the case, NrdH may be an essential gene as well. Since NrdH is not found in humans, a drug that targets NrdH would be able to damage M. tuberculosis cells without hurting the human host.<br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=File:NrdH-NrdE_disulfide.png&diff=2398612File:NrdH-NrdE disulfide.png2015-04-26T19:00:57Z<p>Katelyn Burke: This mechanism shows the passing of electrons from NrdH to NrdE via disulfide bonds.</p>
<hr />
<div>This mechanism shows the passing of electrons from NrdH to NrdE via disulfide bonds.</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2398610Sandbox Reserved 10612015-04-26T18:25:53Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='300' side='right' caption='Micobacterium tuberculosis NrdH' scene='69/694228/Mtnrdh/2'><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH (MtNrdH) is a small glutaredoxin-like protein involved in the electron transport chain in ribonucleotide reduction. Therefore, it is extremely important in DNA production and replication because it helps supply cells with deoxyribonucleotides. Reduction of MtNrdH results in the breaking of an internal disulfide bond at the active site, allowing it to accept electrons and pass them on downstream. Because of its imperative role in ribionucleotide reduction, MtNrdH is thought to be essential to the reproductive integrity of ''M. tuberculosis'', suggesting its role in infectivity and leading to its identification as a possible drug target.<ref name ="Swastik">Swastik, Phulera and Mande, Shekhar C. (2013) The Crystal Structure of Mycobacterium tuberculosis NrdH at 0.87Å Suggests a Possible Mode of Its Activity. Biochemistry 52, 4056-4065.</ref><br />
<br />
== Background ==<br />
<br />
[http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis'']resides in the lungs of a host and upon becoming active, results in a Tuberculosis infection (TB) and the ensuing symptoms of chest pain, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013).<ref name="WHO">"Tuberculosis." Media Centre. World Health Organization, Web. 16 Mar. 2015. Media Centre. <http://www.who.int/mediacentre/factsheets/fs104/en/>.</ref> The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. TB is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative.<ref name="WHO" /><br />
<br />
<br />
== Structure == <br />
<br />
The <scene name='69/694228/Nrdh_structure/1'>MtNrdH structure</scene> determined by x-ray crystallography has 79 residues in a single polypeptide chain. The active site (shown in green) is dominated by a <scene name='69/694228/Nrdh_structure/3'>disulfide bond</scene> between Cys-11 and Cys-14, which serves as the site of reduction by thioredoxin reductase. <ref name="Swastik" /><br />
<br />
Many thioredoxin-like proteins have a similar active site region, which includes the <br />
<scene name='69/694228/Nrdh_structure/6'>thioredoxin fold</scene>, a large turn in the protein structure right before the disulfide bond. The residues directly following the fold, <scene name='69/694228/Nrdh_structure/5'>CVQC</scene>, are the most highly conserved of all areas of the protein across multiple species (Figure 1). <br />
[[Image:Weblogocvqc.png|thumb|center|upright=2.5|'''Figure 1.'''Weblogo diagram showing highly conserved CVQC region of NrdH in four separate protein structures from ''Nocardia seriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.<ref name="weblogo">Crooks GE, Hon G, Chandonia JM, Brenner SE WebLogo: A sequence logo generator,<br />
Genome Research, 14:1188-1190, (2004)</ref>]]<br />
<br />
==== Conformational Changes ====<br />
<br />
Exactly how this structure relates to function is somewhat debated, but it is hypothesized that the fold allows residues preceding the turn to interact with the CVQC region after the turn. A threonine-7 reside directly across the thioredoxin fold from the disulfide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/17'>"A" conformation</scene>, the alcohol oxygen of the threonine side chain (seen as a red ball) points towards the disulfide bond, forming an electrostatic interaction (represented by a short dashed line) between the two that prevents thioredoxin reductase (TrxR) from binding. Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/18'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space and enough electrostatic freedom for the ligand to bind and reduction to occur.<ref name="Swastik" /><br />
<br />
[[Image:Hydrophobic region 2.png|thumb|right| '''Figure 2.'''Hydrophobic region WSGFRP on the surface of MtNrdH (red) next to the active site (green.) Notice that this Hydrophobic region is heavily exposed to solvent. This WSGFRP sequence is thought to help thioredoxin reductase bind for reduction.<ref name="Swastik" /> <ref name="PyMol">The PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.</ref>]]<br />
<br />
Another highly conserved series of residues is the WSGFRP sequence (Figure 3). This nonpolar sequence is found on the surface of the molecule and is exposed to solvent (Figure 2). For this reason, it has been hypothesized that this sequence plays a role in the binding of thioredoxin reductase. <ref name="Swastik" /><br />
<br />
<scene name='69/694227/Arg_68/4'>Arg-68</scene> is responsible for the stabilization of the hydrophobic region of NrdH. Arg-68 has two distinct conformations. In the <scene name='69/694227/Arg_68_conformation_1/4'>first conformation</scene>, Arg-68 is hydrogen bonded to His- 60 and Asp-59. When Arg-68 shifts to its <scene name='69/694227/Arg_68_conformation_2/5'>second conformation</scene>, it breaks its hydrogen bond with Asp-59. <ref name="Swastik" /> This reduction in hydrogen bonding gives the hydrophobic region more flexibility and is thought to occur when NrdH is in its inactive state. <br />
<br />
[[Image:Wsgfrpweblogo.png|thumb|center|upright=2.5|'''Figure 3.'''Weblogo diagram showing highly conserved WSGFRP region of NrdH in four separate protein structures from ''Nocardia seriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.<ref name="weblogo" />]]<br />
<br />
<br />
==== Stabilization ====<br />
The active site of the protein is stabilized through a <scene name='69/696879/Water_coordination/2'>hydrogen bond network</scene> involving the two highly conserved series of residues, CVQC (green) and WSGFRP (red). A water molecule appears to be a key part of the H-bonding network. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<ref name="Swastik" /><br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called [http://www.proteopedia.org/wiki/index.php/Ribonucleotide_reductase ribonucleotide reductase (RNR)] to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes.<ref name ="Kolberg">Kolberg, M., et al. (2004) Structure, function, and mechanism of ribonucleotide reductases. Biochim. Biophys. Acta 1699 (1−2), 1−34.</ref> Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). Ribonucleotide reductase utilizes free thiols to reduce NDP to dNDP. After both of the free thiols give up their electrons, they form a disulfide bond. To be able to perform another round of reduction, the disulfide bond needs to be reduced into free thiols again. In class Ia, RNR is reduced by either glutadoxin or thioredoxin, which are first reduced by glutadoxin reductase and thioredoxin reductase, respectively.<ref>Nelson, David L., and Michael M. Cox. Lehninger Principles of Biochemistry. 5th ed. New York: W.H. Freeman, 2008. 888-889.</ref> In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH (Figure 4). Like ribonucleotide reductase, NrdE and NrdH both use the making and breaking of disulfide bonds to pass electrons down the chain. Thioredoxin reductase uses NADPH to reduce NrdH <ref name="Makhlynets" />. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <ref name="Kolberg" /><br />
<br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|'''Figure 4.'''Ribonucleotide Reduction Class Ib general mechanism.<ref name="Makhlynets">Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref> The role of NrdH is highlighted.]] <br />
<br />
== Relevance ==<br />
<br />
Like most NrdHs, MtNrdH is similar in sequence to glutaredoxins, but structurally similar to thioredoxins (Figure 5). MtNrdH also accepts electrons from thioredoxin reductase, a characteristic of thioredoxins, but not glutaredoxins.<ref name="Swastik" /> [[Image:Image-Super imposed molecules.png|thumb|left|'''Figure 5.'''Structural comparison of NrdHs with "thioredoxin folds": ''E. Coli'' NrdH (green), ''C. ammoniagenes'' NrdH (blue), ''M. tuberculosis'' NrdH (red)<ref name="PyMol" />]] <br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', ''S. dysenteriae'', and ''C. glutamicium''<ref>Wang, M. et al. Mol Cell Proteomics 2012, doi:10.1074/mcp.O111.014704. http://pax-db.org/#!search?q=NrdH%250A</ref> <ref>Si, M.-R., Zhang, L., Yang, Z.-F., Xu, Y.-X., Liu, Y.-B., Jiang, C.-Y., … Liu, S.-J. (2014). NrdH Redoxin Enhances Resistance to Multiple Oxidative Stresses by Acting as a Peroxidase Cofactor in Corynebacterium glutamicum. Applied and Environmental Microbiology, 80(5), 1750–1762. doi:10.1128/AEM.03654-13</ref> In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or thioredoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. <ref name="Swastik" /> If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the [http://en.wikipedia.org/wiki/RNA_world RNA Wold Hypothesis], specifically describing the time frame of emergence of DNA based life. <br />
<br />
==Possible Drug Target==<br />
<br />
MtNrdH can serve as a potential drug target to treat tuberculosis. The genes encoding NrdE and NrdF2, a cofactor in class 1b ribonucleotide reduction, are essential for growth of M. tuberculosis in vitro.<ref>Mowa, M. B., et al. (2009) Function and regulation of class I ribonucleotide reductase-encoding genes in mycobacteria. J. Bacteriol. 191 (3), 985−995</ref> This suggests that M. tuberculosis relies solely on class Ib ribonucleotide reduction. If that is the case, NrdH may be an essential gene as well. Since NrdH is not found in humans, a drug that targets NrdH would be able to damage M. tuberculosis cells without hurting the human host.<br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=File:Hydrophobic_region_2.png&diff=2398609File:Hydrophobic region 2.png2015-04-26T18:19:09Z<p>Katelyn Burke: Hydrophobic region of MtNrdH (red) next to the active site (green). Notice that this hydrophobic patch is heavily exposed to solvent.</p>
<hr />
<div>Hydrophobic region of MtNrdH (red) next to the active site (green). Notice that this hydrophobic patch is heavily exposed to solvent.</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2398481Sandbox Reserved 10612015-04-24T13:47:33Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='220' side='right' caption='Micobacterium tuberculosis NrdH' scene='69/694228/Mtnrdh/2'><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH (MtNrdH) is a small glutaredoxin-like protein involved in the electron transport chain in ribonucleotide reduction. Therefore, it is extremely important in DNA production and replication because it helps supply cells with deoxyribonucleotides. Reduction of MtNrdH results in the breaking of an internal disulfide bond at the active site, allowing it to accept electrons and pass them on downstream. Because of its imperative role in ribionucleotide reduction, MtNrdH is thought to be essential to the reproductive integrity of ''M. tuberculosis'', suggesting its role in infectivity and leading to its identification as a possible drug target.<ref name ="Swastik">Swastik, Phulera and Mande, Shekhar C. (2013) The Crystal Structure of Mycobacterium tuberculosis NrdH at 0.87Å Suggests a Possible Mode of Its Activity. Biochemistry 52, 4056-4065.</ref><br />
<br />
== Background ==<br />
<br />
[http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis'']resides in the lungs of a host and upon becoming active, results in a Tuberculosis infection (TB) and the ensuing symptoms of chest pain, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013).<ref name="WHO">"Tuberculosis." Media Centre. World Health Organization, Web. 16 Mar. 2015. Media Centre. <http://www.who.int/mediacentre/factsheets/fs104/en/>.</ref> The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. TB is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative.<ref name="WHO" /><br />
<br />
<br />
== Structure == <br />
<br />
The <scene name='69/694228/Nrdh_structure/1'>MtNrdH structure</scene> determined by x-ray crystallography has 79 residues in a single polypeptide chain. The active site (shown in green) is dominated by a <scene name='69/694228/Nrdh_structure/3'>disulfide bond</scene> between Cys-11 and Cys-14, which serves as the site of reduction by thioredoxin reductase. <ref name="Swastik" /><br />
<br />
Many thioredoxin-like proteins have a similar active site region, which includes the <br />
<scene name='69/694228/Nrdh_structure/6'>thioredoxin fold</scene>, a large turn in the protein structure right before the disulfide bond. The residues directly following the fold, <scene name='69/694228/Nrdh_structure/5'>CVQC</scene>, are the most highly conserved of all areas of the protein across multiple species. <br />
[[Image:Weblogocvqc.png|thumb|center|upright=2.5|'''Figure 1.'''Weblogo diagram showing highly conserved CVQC region of NrdH in four separate protein structures from ''Nocardia seriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.<ref name="weblogo">Crooks GE, Hon G, Chandonia JM, Brenner SE WebLogo: A sequence logo generator,<br />
Genome Research, 14:1188-1190, (2004)</ref>]]<br />
<br />
==== Conformational Changes ====<br />
<br />
Exactly how this structure relates to function is somewhat debated, but it is hypothesized that the fold allows residues preceding the turn to interact with the CVQC motif after the turn. A threonine-7 reside directly across the thioredoxin fold from the disulfide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/17'>"A" conformation</scene>, the alcohol oxygen of the threonine side chain (seen as a red ball) points towards the disulfide bond, forming an electrostatic interaction (represented by a short dashed line) between the two that prevents thioredoxin reductase from binding. Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/16'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space and enough electrostatic freedom for the ligand to bind and reduction to occur.<ref name="Swastik" /><br />
<br />
[[Image:Hydrophobic region pic.png|thumb|right| '''Figure 2.'''Hydrophobic region WSGFRP on the surface of MtNrdH (red) bound to ligand (green).<ref name="PyMol">The PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.</ref>]]<br />
<br />
Another highly conserved series of residues is the WSGFRP sequence. This nonpolar sequence is found on the surface of the molecule and is exposed to solvent. For this reason, it has been hypothesized that this sequence plays a role in the binding of thioredoxin reductase. <ref name="Swastik" /><br />
<br />
<scene name='69/694227/Arg_68/4'>Arg-68</scene> is responsible for the stabilization of the hydrophobic region of NrdH. Arg-68 has two distinct conformations. In the <scene name='69/694227/Arg_68_conformation_1/4'>first conformation</scene>, Arg-68 is hydrogen bonded to His- 60 and Asp-59. When Arg-68 shifts to its <scene name='69/694227/Arg_68_conformation_2/5'>second conformation</scene>, it breaks its hydrogen bond with Asp-59. <ref name="Swastik" /> This reduction in hydrogen bonding gives the hydrophobic region more flexibility and is thought to occur when NrdH is in its inactive state. <br />
<br />
[[Image:Wsgfrpweblogo.png|thumb|center|upright=2.5|'''Figure 3.'''Weblogo diagram showing highly conserved WSGFRP region of NrdH in four separate protein structures from ''Nocardia seriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.<ref name="weblogo" />]]<br />
<br />
<br />
==== Stabilization ====<br />
The active site of the protein is stabilized through a <scene name='69/696879/Water_coordination/1'>hydrogen bond network</scene> involving the two highly conserved series of residues, CVQC (green) and WSGFRP (yellow). A water molecule appears to be a key part of the H-bonding network. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<ref name="Swastik" /><br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called [http://www.proteopedia.org/wiki/index.php/Ribonucleotide_reductase ribonucleotide reductase (RNR)] to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes.<ref name ="Kolberg">Kolberg, M., et al. (2004) Structure, function, and mechanism of ribonucleotide reductases. Biochim. Biophys. Acta 1699 (1−2), 1−34.</ref> Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). Ribonucleotide reductase utilizes free thiols to reduce NDP to dNDP. After both of the free thiols give up their electrons, they form a disulfide bond. To be able to perform another round of reduction, the disulfide bond needs to be reduced into free thiols again. In class Ia, RNR is reduced by either glutadoxin or thioredoxin, which are first reduced by glutadoxin reductase and thioredoxin reductase, respectively.<ref>Nelson, David L., and Michael M. Cox. Lehninger Principles of Biochemistry. 5th ed. New York: W.H. Freeman, 2008. 888-889.</ref> In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH (Figure 4). Like ribonucleotide reductase, NrdE and NrdH both use the making and breaking of disulfide bonds to pass electrons down the chain. Thioredoxin reductase uses NADPH to reduce NrdH <ref name="Makhlynets" />. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <ref name="Kolberg" /><br />
<br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|'''Figure 4.'''Ribonucleotide Reduction Class Ib general mechanism.<ref name="Makhlynets">Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref> The role of NrdH is highlighted.]] <br />
<br />
== Relevance ==<br />
<br />
Like most NrdHs, MtNrdH is similar in sequence to glutaredoxins, but structurally similar to thioredoxins. MtNrdH also accepts electrons from thioredoxin reductase, a characteristic of thioredoxins, but not glutaredoxins.<ref name="Swastik" /> [[Image:Image-Super imposed molecules.png|thumb|left|'''Figure 5.'''Structural comparison of NrdHs with "thioredoxin folds": ''E. Coli'' NrdH (green), ''C. ammoniagenes'' NrdH (blue), ''M. tuberculosis'' NrdH (red)<ref name="PyMol" />]] <br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', ''S. dysenteriae'', and ''C. glutamicium''<ref>Wang, M. et al. Mol Cell Proteomics 2012, doi:10.1074/mcp.O111.014704. http://pax-db.org/#!search?q=NrdH%250A</ref> <ref>Si, M.-R., Zhang, L., Yang, Z.-F., Xu, Y.-X., Liu, Y.-B., Jiang, C.-Y., … Liu, S.-J. (2014). NrdH Redoxin Enhances Resistance to Multiple Oxidative Stresses by Acting as a Peroxidase Cofactor in Corynebacterium glutamicum. Applied and Environmental Microbiology, 80(5), 1750–1762. doi:10.1128/AEM.03654-13</ref> In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or thioredoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. <ref name="Swastik" /> If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
==Possible Drug Target==<br />
<br />
MtNrdH can serve as a potential drug target to treat tuberculosis. The genes encoding NrdE and NrdF2, a cofactor in class 1b ribonucleotide reduction, are essential for growth of M. tuberculosis in vitro.<ref>Mowa, M. B., et al. (2009) Function and regulation of class I ribonucleotide reductase-encoding genes in mycobacteria. J. Bacteriol. 191 (3), 985−995</ref> This suggest that M. tuberculosis relies solely on class Ib ribonucleotide reduction. If that is the case, NrdH may be an essential gene as well. Since NrdH is not found in humans, a drug that targets NrdH would be able to damage M. tuberculosis cells without hurting the human host.<br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2398480Sandbox Reserved 10612015-04-24T13:45:13Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='220' side='right' caption='Micobacterium tuberculosis NrdH' scene='69/694228/Mtnrdh/2'><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH (MtNrdH) is a small glutaredoxin-like protein involved in the electron transport chain in ribonucleotide reduction. Therefore, it is extremely important in DNA production and replication because it helps supply cells with deoxyribonucleotides. Reduction of MtNrdH results in the breaking of an internal disulfide bond at the active site, allowing it to accept electrons and pass them on downstream. Because of its imperative role in ribionucleotide reduction, MtNrdH is thought to be essential to the reproductive integrity of ''M. tuberculosis'', suggesting its role in infectivity and leading to its identification as a possible drug target.<ref name ="Swastik">Swastik, Phulera and Mande, Shekhar C. (2013) The Crystal Structure of Mycobacterium tuberculosis NrdH at 0.87Å Suggests a Possible Mode of Its Activity. Biochemistry 52, 4056-4065.</ref><br />
<br />
== Background ==<br />
<br />
[http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis'']resides in the lungs of a host and upon becoming active, results in a Tuberculosis infection (TB) and the ensuing symptoms of chest pain, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013).<ref name="WHO">"Tuberculosis." Media Centre. World Health Organization, Web. 16 Mar. 2015. Media Centre. <http://www.who.int/mediacentre/factsheets/fs104/en/>.</ref> The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. TB is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative.<ref name="WHO" /><br />
<br />
<br />
== Structure == <br />
<br />
The <scene name='69/694228/Nrdh_structure/1'>MtNrdH structure</scene> determined by x-ray crystallography has 79 residues in a single polypeptide chain. The active site (shown in green) is dominated by a <scene name='69/694228/Nrdh_structure/3'>disulfide bond</scene> between Cys-11 and Cys-14, which serves as the site of reduction by thioredoxin reductase. <ref name="Swastik" /><br />
<br />
Many thioredoxin-like proteins have a similar active site region, which includes the <br />
<scene name='69/694228/Nrdh_structure/6'>thioredoxin fold</scene>, a large turn in the protein structure right before the disulfide bond. The residues directly following the fold, <scene name='69/694228/Nrdh_structure/5'>CVQC</scene>, are the most highly conserved of all areas of the protein across multiple species. <br />
[[Image:Weblogocvqc.png|thumb|center|upright=2.5|'''Figure 1.'''Weblogo diagram showing highly conserved CVQC region of NrdH in four separate protein structures from ''Nocardia seriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.<ref name="weblogo">Crooks GE, Hon G, Chandonia JM, Brenner SE WebLogo: A sequence logo generator,<br />
Genome Research, 14:1188-1190, (2004)</ref>]]<br />
<br />
==== Conformational Changes ====<br />
<br />
Exactly how this structure relates to function is somewhat debated, but it is hypothesized that the fold allows residues preceding the turn to interact with the CVQC motif after the turn. A threonine-7 reside directly across the thioredoxin fold from the disulfide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/17'>"A" conformation</scene>, the alcohol oxygen of the threonine side chain (seen as a red ball) points towards the disulfide bond, forming an electrostatic interaction (represented by a short dashed line) between the two that prevents thioredoxin reductase from binding. Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/16'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space and enough electrostatic freedom for the ligand to bind and reduction to occur.<ref name="Swastik" /><br />
<br />
[[Image:Hydrophobic region pic.png|thumb|right| '''Figure 2.'''Hydrophobic region WSGFRP on the surface of MtNrdH (red) bound to ligand (green).<ref name="PyMol">The PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.</ref>]]<br />
<br />
Another highly conserved series of residues is the WSGFRP sequence. This nonpolar sequence is found on the surface of the molecule and is exposed to solvent. For this reason, it has been hypothesized that this sequence plays a role in the binding of thioredoxin reductase. <ref name="Swastik" /><br />
<br />
<scene name='69/694227/Arg_68/4'>Arg-68</scene> is responsible for the stabilization of the hydrophobic region of NrdH. Arg-68 has two distinct conformations. In the <scene name='69/694227/Arg_68_conformation_1/4'>first conformation</scene>, Arg-68 is hydrogen bonded to His- 60 and Asp-59. When Arg-68 shifts to its <scene name='69/694227/Arg_68_conformation_2/5'>second conformation</scene>, it breaks its hydrogen bond with Asp-59. <ref name="Swastik" /> This reduction in hydrogen bonding gives the hydrophobic region more flexibility and is thought to occur when NrdH is in its inactive state. <br />
<br />
[[Image:Wsgfrpweblogo.png|thumb|center|upright=2.5|'''Figure 3.'''Weblogo diagram showing highly conserved WSGFRP region of NrdH in four separate protein structures from ''Nocardia seriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.<ref name="weblogo" />]]<br />
<br />
<br />
==== Stabilization ====<br />
The active site of the protein is stabilized through a <scene name='69/696879/Water_coordination/1'>hydrogen bond network</scene> involving the two highly conserved series of residues, CVQC (green) and WSGFRP (yellow). A water molecule appears to be a key part of the H-bonding network. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<ref name="Swastik" /><br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called [http://www.proteopedia.org/wiki/index.php/Ribonucleotide_reductase ribonucleotide reductase (RNR)] to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes.<ref name ="Kolberg">Kolberg, M., et al. (2004) Structure, function, and mechanism of ribonucleotide reductases. Biochim. Biophys. Acta 1699 (1−2), 1−34.</ref> Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). Ribonucleotide reductase utilizes free thiols to reduce NDP to dNDP. After both of the free thiols give up their electrons, they form a disulfide bond. To be able to perform another round of reduction, the disulfide bond needs to be reduced into free thiols again. In class Ia, RNR is reduced by either glutadoxin or thioredoxin, which are first reduced by glutadoxin reductase and thioredoxin reductase, respectively.<ref>Nelson, David L., and Michael M. Cox. Lehninger Principles of Biochemistry. 5th ed. New York: W.H. Freeman, 2008. 888-889.</ref> In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH (Figure 4). Like ribonucleotide reductase, NrdE and NrdH both use the making and breaking of disulfide bonds to pass electrons down the chain. Thioredoxin reductase uses an NADPH group to reduce NrdH <ref name="Makhlynets" />. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <ref name="Kolberg" /><br />
<br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|'''Figure 4.'''Ribonucleotide Reduction Class Ib general mechanism.<ref name="Makhlynets">Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref> The role of NrdH is highlighted.]] <br />
<br />
== Relevance ==<br />
<br />
Like most NrdHs, MtNrdH is similar in sequence to glutaredoxins, but structurally similar to thioredoxins. MtNrdH also accepts electrons from thioredoxin reductase, a characteristic of thioredoxins, but not glutaredoxins.<ref name="Swastik" /> [[Image:Image-Super imposed molecules.png|thumb|left|'''Figure 5.'''Structural comparison of NrdHs with "thioredoxin folds": ''E. Coli'' NrdH (green), ''C. ammoniagenes'' NrdH (blue), ''M. tuberculosis'' NrdH (red)<ref name="PyMol" />]] <br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', ''S. dysenteriae'', and ''C. glutamicium''<ref>Wang, M. et al. Mol Cell Proteomics 2012, doi:10.1074/mcp.O111.014704. http://pax-db.org/#!search?q=NrdH%250A</ref> <ref>Si, M.-R., Zhang, L., Yang, Z.-F., Xu, Y.-X., Liu, Y.-B., Jiang, C.-Y., … Liu, S.-J. (2014). NrdH Redoxin Enhances Resistance to Multiple Oxidative Stresses by Acting as a Peroxidase Cofactor in Corynebacterium glutamicum. Applied and Environmental Microbiology, 80(5), 1750–1762. doi:10.1128/AEM.03654-13</ref> In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or thioredoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. <ref name="Swastik" /> If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
==Possible Drug Target==<br />
<br />
MtNrdH can serve as a potential drug target to treat tuberculosis. The genes encoding NrdE and NrdF2, a cofactor in class 1b ribonucleotide reduction, are essential for growth of M. tuberculosis in vitro.<ref>Mowa, M. B., et al. (2009) Function and regulation of class I ribonucleotide reductase-encoding genes in mycobacteria. J. Bacteriol. 191 (3), 985−995</ref> This suggest that M. tuberculosis relies solely on class Ib ribonucleotide reduction. If that is the case, NrdH may be an essential gene as well. Since NrdH is not found in humans, a drug that targets NrdH would be able to damage M. tuberculosis cells without hurting the human host.<br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2398479Sandbox Reserved 10612015-04-24T13:27:41Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='220' side='right' caption='Micobacterium tuberculosis NrdH' scene='69/694228/Mtnrdh/2'><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH (MtNrdH) is a small glutaredoxin-like protein involved in the electron transport chain in ribonucleotide reduction. Therefore, it is extremely important in DNA production and replication because it helps supply cells with deoxyribonucleotides. Reduction of MtNrdH results in the breaking of an internal disulfide bond at the active site, allowing it to accept electrons and pass them on downstream. Because of its imperative role in ribionucleotide reduction, MtNrdH is thought to be essential to the reproductive integrity of ''M. tuberculosis'', suggesting its role in infectivity and leading to its identification as a possible drug target.<ref name ="Swastik">Swastik, Phulera and Mande, Shekhar C. (2013) The Crystal Structure of Mycobacterium tuberculosis NrdH at 0.87Å Suggests a Possible Mode of Its Activity. Biochemistry 52, 4056-4065.</ref><br />
<br />
== Background ==<br />
<br />
[http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis'']resides in the lungs of a host and upon becoming active, results in a Tuberculosis infection (TB) and the ensuing symptoms of chest pain, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013).<ref name="WHO">"Tuberculosis." Media Centre. World Health Organization, Web. 16 Mar. 2015. Media Centre. <http://www.who.int/mediacentre/factsheets/fs104/en/>.</ref> The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. TB is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative.<ref name="WHO" /><br />
<br />
<br />
== Structure == <br />
<br />
The <scene name='69/694228/Nrdh_structure/1'>MtNrdH structure</scene> determined by x-ray crystallography has 79 residues in a single polypeptide chain. The active site (shown in green) is dominated by a <scene name='69/694228/Nrdh_structure/3'>disulfide bond</scene> between Cys-11 and Cys-14, which serves as the site of reduction by thioredoxin reductase. <ref name="Swastik" /><br />
<br />
Many thioredoxin-like proteins have a similar active site region, which includes the <br />
<scene name='69/694228/Nrdh_structure/6'>thioredoxin fold</scene>, a large turn in the protein structure right before the disulfide bond. The residues directly following the fold, <scene name='69/694228/Nrdh_structure/5'>CVQC</scene>, are the most highly conserved of all areas of the protein across multiple species. <br />
[[Image:Weblogocvqc.png|thumb|center|upright=2.5|'''Figure 1.'''Weblogo diagram showing highly conserved CVQC region of NrdH in four separate protein structures from ''Nocardia seriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.<ref name="weblogo">Crooks GE, Hon G, Chandonia JM, Brenner SE WebLogo: A sequence logo generator,<br />
Genome Research, 14:1188-1190, (2004)</ref>]]<br />
<br />
==== Conformational Changes ====<br />
<br />
Exactly how this structure relates to function is somewhat debated, but it is hypothesized that the fold allows residues preceding the turn to interact with the CVQC motif after the turn. A threonine-7 reside directly across the thioredoxin fold from the disulfide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/17'>"A" conformation</scene>, the alcohol oxygen of the threonine side chain (seen as a red ball) points towards the disulfide bond, forming an electrostatic interaction (represented by a short dashed line) between the two that prevents thioredoxin reductase from binding. Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/16'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space and enough electrostatic freedom for the ligand to bind and reduction to occur.<ref name="Swastik" /><br />
<br />
[[Image:Hydrophobic region pic.png|thumb|right| '''Figure 2.'''Hydrophobic region WSGFRP on the surface of MtNrdH (red) bound to ligand (green).<ref name="PyMol">The PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.</ref>]]<br />
<br />
Another highly conserved series of residues is the WSGFRP sequence. This nonpolar sequence is found on the surface of the molecule and is exposed to solvent. For this reason, it has been hypothesized that this sequence plays a role in the binding of thioredoxin reductase. <ref name="Swastik" /><br />
<br />
<scene name='69/694227/Arg_68/4'>Arg-68</scene> is responsible for the stabilization of the hydrophobic region of NrdH. Arg-68 has two distinct conformations. In the <scene name='69/694227/Arg_68_conformation_1/4'>first conformation</scene>, Arg-68 is hydrogen bonded to His- 60 and Asp-59. When Arg-68 shifts to its <scene name='69/694227/Arg_68_conformation_2/5'>second conformation</scene>, it breaks its hydrogen bond with Asp-59. <ref name="Swastik" /> This reduction in hydrogen bonding gives the hydrophobic region more flexibility and is thought to occur when NrdH is in its inactive state. <br />
<br />
[[Image:Wsgfrpweblogo.png|thumb|center|upright=2.5|'''Figure 3.'''Weblogo diagram showing highly conserved WSGFRP region of NrdH in four separate protein structures from ''Nocardia seriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.<ref name="weblogo" />]]<br />
<br />
<br />
==== Stabilization ====<br />
The active site of the protein is stabilized through a <scene name='69/696879/Water_coordination/1'>hydrogen bond network</scene> involving the two highly conserved series of residues, CVQC (green) and WSGFRP (yellow). A water molecule appears to be a key part of the H-bonding network. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<ref name="Swastik" /><br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called [http://www.proteopedia.org/wiki/index.php/Ribonucleotide_reductase ribonucleotide reductase (RNR)] to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes.<ref name ="Kolberg">Kolberg, M., et al. (2004) Structure, function, and mechanism of ribonucleotide reductases. Biochim. Biophys. Acta 1699 (1−2), 1−34.</ref> Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thioredoxin, which are first reduced by glutadoxin reductase and thioredoxin reductase, respectively.<ref>Nelson, David L., and Michael M. Cox. Lehninger Principles of Biochemistry. 5th ed. New York: W.H. Freeman, 2008. 888-889.</ref> In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <ref name="Kolberg" /><br />
<br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|'''Figure 4.'''Ribonucleotide Reduction Class Ib general mechanism.<ref>Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref> The role of NrdH is highlighted.]] <br />
<br />
== Relevance ==<br />
<br />
Like most NrdHs, MtNrdH is similar in sequence to glutaredoxins, but structurally similar to thioredoxins. MtNrdH also accepts electrons from thioredoxin reductase, a characteristic of thioredoxins, but not glutaredoxins.<ref name="Swastik" /> [[Image:Image-Super imposed molecules.png|thumb|left|'''Figure 5.'''Structural comparison of NrdHs with "thioredoxin folds": ''E. Coli'' NrdH (green), ''C. ammoniagenes'' NrdH (blue), ''M. tuberculosis'' NrdH (red)<ref name="PyMol" />]] <br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', ''S. dysenteriae'', and ''C. glutamicium''<ref>Wang, M. et al. Mol Cell Proteomics 2012, doi:10.1074/mcp.O111.014704. http://pax-db.org/#!search?q=NrdH%250A</ref> <ref>Si, M.-R., Zhang, L., Yang, Z.-F., Xu, Y.-X., Liu, Y.-B., Jiang, C.-Y., … Liu, S.-J. (2014). NrdH Redoxin Enhances Resistance to Multiple Oxidative Stresses by Acting as a Peroxidase Cofactor in Corynebacterium glutamicum. Applied and Environmental Microbiology, 80(5), 1750–1762. doi:10.1128/AEM.03654-13</ref> In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or thioredoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. <ref name="Swastik" /> If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
==Possible Drug Target==<br />
<br />
MtNrdH can serve as a potential drug target to treat tuberculosis. The genes encoding NrdE and NrdF2, a cofactor in class 1b ribonucleotide reduction, are essential for growth of M. tuberculosis in vitro.<ref>Mowa, M. B., et al. (2009) Function and regulation of class I ribonucleotide reductase-encoding genes in mycobacteria. J. Bacteriol. 191 (3), 985−995</ref> This suggest that M. tuberculosis relies solely on class Ib ribonucleotide reduction. If that is the case, NrdH may be an essential gene as well. Since NrdH is not found in humans, a drug that targets NrdH would be able to damage M. tuberculosis cells without hurting the human host.<br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2398478Sandbox Reserved 10612015-04-24T13:22:31Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='300' side='right' caption='Micobacterium tuberculosis NrdH' scene='69/694228/Mtnrdh/2'><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH (MtNrdH) is a small glutaredoxin-like protein involved in the electron transport chain in ribonucleotide reduction. Therefore, it is extremely important in DNA production and replication because it helps supply cells with deoxyribonucleotides. Reduction of MtNrdH results in the breaking of an internal disulfide bond at the active site, allowing it to accept electrons and pass them on downstream. Because of its imperative role in ribionucleotide reduction, MtNrdH is thought to be essential to the reproductive integrity of ''M. tuberculosis'', suggesting its role in infectivity and leading to its identification as a possible drug target.<ref name ="Swastik">Swastik, Phulera and Mande, Shekhar C. (2013) The Crystal Structure of Mycobacterium tuberculosis NrdH at 0.87Å Suggests a Possible Mode of Its Activity. Biochemistry 52, 4056-4065.</ref><br />
<br />
== Background ==<br />
<br />
[http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis'']resides in the lungs of a host and upon becoming active, results in a Tuberculosis infection (TB) and the ensuing symptoms of chest pain, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013).<ref name="WHO">"Tuberculosis." Media Centre. World Health Organization, Web. 16 Mar. 2015. Media Centre. <http://www.who.int/mediacentre/factsheets/fs104/en/>.</ref> The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. TB is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative.<ref name="WHO" /><br />
<br />
<br />
== Structure == <br />
<br />
The <scene name='69/694228/Nrdh_structure/1'>MtNrdH structure</scene> determined by x-ray crystallography has 79 residues in a single polypeptide chain. The active site (shown in green) is dominated by a <scene name='69/694228/Nrdh_structure/3'>disulfide bond</scene> between Cys-11 and Cys-14, which serves as the site of reduction by thioredoxin reductase. <ref name="Swastik" /><br />
<br />
Many thioredoxin-like proteins have a similar active site region, which includes the <br />
<scene name='69/694228/Nrdh_structure/6'>thioredoxin fold</scene>, a large turn in the protein structure right before the disulfide bond. The residues directly following the fold, <scene name='69/694228/Nrdh_structure/5'>CVQC</scene>, are the most highly conserved of all areas of the protein across multiple species. <br />
[[Image:Weblogocvqc.png|thumb|center|upright=2.5|'''Figure 1.'''Weblogo diagram showing highly conserved CVQC region of NrdH in four separate protein structures from ''Nocardia seriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.<ref name="weblogo">Crooks GE, Hon G, Chandonia JM, Brenner SE WebLogo: A sequence logo generator,<br />
Genome Research, 14:1188-1190, (2004)</ref>]]<br />
<br />
==== Conformational Changes ====<br />
<br />
Exactly how this structure relates to function is somewhat debated, but it is hypothesized that the fold allows residues preceding the turn to interact with the CVQC motif after the turn. A threonine-7 reside directly across the thioredoxin fold from the disulfide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/17'>"A" conformation</scene>, the alcohol oxygen of the threonine side chain (seen as a red ball) points towards the disulfide bond, forming an electrostatic interaction (represented by a short dashed line) between the two that prevents thioredoxin reductase from binding. Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/16'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space and enough electrostatic freedom for the ligand to bind and reduction to occur.<ref name="Swastik" /><br />
<br />
[[Image:Hydrophobic region pic.png|thumb|right| '''Figure 2.'''Hydrophobic region WSGFRP on the surface of MtNrdH (red) bound to ligand (green).<ref name="PyMol">The PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.</ref>]]<br />
<br />
Another highly conserved series of residues is the WSGFRP sequence. This nonpolar sequence is found on the surface of the molecule and is exposed to solvent. For this reason, it has been hypothesized that this sequence plays a role in the binding of thioredoxin reductase. <ref name="Swastik" /><br />
<br />
<scene name='69/694227/Arg_68/4'>Arg-68</scene> is responsible for the stabilization of the hydrophobic region of NrdH. Arg-68 has two distinct conformations. In the <scene name='69/694227/Arg_68_conformation_1/4'>first conformation</scene>, Arg-68 is hydrogen bonded to His- 60 and Asp-59. When Arg-68 shifts to its <scene name='69/694227/Arg_68_conformation_2/5'>second conformation</scene>, it breaks its hydrogen bond with Asp-59. <ref name="Swastik" /> This reduction in hydrogen bonding gives the hydrophobic region more flexibility and is thought to occur when NrdH is in its inactive state. <br />
<br />
[[Image:Wsgfrpweblogo.png|thumb|center|upright=2.5|'''Figure 3.'''Weblogo diagram showing highly conserved WSGFRP region of NrdH in four separate protein structures from ''Nocardia seriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.<ref name="weblogo" />]]<br />
<br />
<br />
==== Stabilization ====<br />
The active site of the protein is stabilized through a <scene name='69/696879/Water_coordination/1'>hydrogen bond network</scene> involving the two highly conserved series of residues, CVQC (green) and WSGFRP (yellow). A water molecule appears to be a key part of the H-bonding network. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<ref name="Swastik" /><br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called [http://www.proteopedia.org/wiki/index.php/Ribonucleotide_reductase ribonucleotide reductase (RNR)] to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes.<ref name ="Kolberg">Kolberg, M., et al. (2004) Structure, function, and mechanism of ribonucleotide reductases. Biochim. Biophys. Acta 1699 (1−2), 1−34.</ref> Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thioredoxin, which are first reduced by glutadoxin reductase and thioredoxin reductase, respectively.<ref>Nelson, David L., and Michael M. Cox. Lehninger Principles of Biochemistry. 5th ed. New York: W.H. Freeman, 2008. 888-889.</ref> In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <ref name="Kolberg" /><br />
<br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|'''Figure 4.'''Ribonucleotide Reduction Class Ib general mechanism.<ref>Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref> The role of NrdH is highlighted.]] <br />
<br />
== Relevance ==<br />
<br />
Like most NrdHs, MtNrdH is similar in sequence to glutaredoxins, but structurally similar to thioredoxins. MtNrdH also accepts electrons from thioredoxin reductase, a characteristic of thioredoxins, but not glutaredoxins.<ref name="Swastik" /> [[Image:Image-Super imposed molecules.png|thumb|left|'''Figure 5.'''Structural comparison of NrdHs with "thioredoxin folds": ''E. Coli'' NrdH (green), ''C. ammoniagenes'' NrdH (blue), ''M. tuberculosis'' NrdH (red)<ref name="PyMol" />]] <br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', ''S. dysenteriae'', and ''C. glutamicium''<ref>Wang, M. et al. Mol Cell Proteomics 2012, doi:10.1074/mcp.O111.014704. http://pax-db.org/#!search?q=NrdH%250A</ref> <ref>Si, M.-R., Zhang, L., Yang, Z.-F., Xu, Y.-X., Liu, Y.-B., Jiang, C.-Y., … Liu, S.-J. (2014). NrdH Redoxin Enhances Resistance to Multiple Oxidative Stresses by Acting as a Peroxidase Cofactor in Corynebacterium glutamicum. Applied and Environmental Microbiology, 80(5), 1750–1762. doi:10.1128/AEM.03654-13</ref> In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or thioredoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. <ref name="Swastik" /> If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
==Possible Drug Target==<br />
<br />
MtNrdH can serve as a potential drug target to treat tuberculosis. The genes encoding NrdE and NrdF2, a cofactor in class 1b ribonucleotide reduction, are essential for growth of M. tuberculosis in vitro.<ref>Mowa, M. B., et al. (2009) Function and regulation of class I ribonucleotide reductase-encoding genes in mycobacteria. J. Bacteriol. 191 (3), 985−995</ref> This suggest that M. tuberculosis relies solely on class Ib ribonucleotide reduction. If that is the case, NrdH may be an essential gene as well. Since NrdH is not found in humans, a drug that targets NrdH would be able to damage M. tuberculosis cells without hurting the human host.<br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2398477Sandbox Reserved 10612015-04-24T13:18:08Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='300' side='right' caption='Micobacterium tuberculosis NrdH' scene='69/694228/Mtnrdh/2'><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH (MtNrdH) is a small glutaredoxin-like protein involved in the electron transport chain in ribonucleotide reduction. Therefore, it is extremely important in DNA production and replication because it helps supply cells with deoxyribonucleotides. Reduction of MtNrdH results in the breaking of an internal disulfide bond at the active site, allowing it to accept electrons and pass them on downstream. Because of its imperative role in ribionucleotide reduction, MtNrdH is thought to be essential to the reproductive integrity of ''M. tuberculosis'', suggesting its role in infectivity and leading to its identification as a possible drug target.<ref name ="Swastik">Swastik, Phulera and Mande, Shekhar C. (2013) The Crystal Structure of Mycobacterium tuberculosis NrdH at 0.87Å Suggests a Possible Mode of Its Activity. Biochemistry 52, 4056-4065.</ref><br />
<br />
== Background ==<br />
<br />
[http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis'']resides in the lungs of a host and upon becoming active, results in a Tuberculosis infection (TB) and the ensuing symptoms of chest pain, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013).<ref name="WHO">"Tuberculosis." Media Centre. World Health Organization, Web. 16 Mar. 2015. Media Centre. <http://www.who.int/mediacentre/factsheets/fs104/en/>.</ref> The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. TB is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative.<ref name="WHO" /><br />
<br />
<br />
== Structure == <br />
<br />
The <scene name='69/694228/Nrdh_structure/1'>MtNrdH structure</scene> determined by x-ray crystallography has 79 residues in a single polypeptide chain. The active site (shown in green) is dominated by a <scene name='69/694228/Nrdh_structure/3'>disulfide bond</scene> between Cys-11 and Cys-14, which serves as the site of reduction by thioredoxin reductase. <ref name="Swastik" /><br />
<br />
Many thioredoxin-like proteins have a similar active site region, which includes the <br />
<scene name='69/694228/Nrdh_structure/6'>thioredoxin fold</scene>, a large turn in the protein structure right before the disulfide bond. The residues directly following the fold, <scene name='69/694228/Nrdh_structure/5'>CVQC</scene>, are the most highly conserved of all areas of the protein across multiple species. <br />
[[Image:Weblogocvqc.png|thumb|center|upright=2.5|Weblogo diagram showing highly conserved CVQC region of NrdH in four separate protein structures from ''Nocardia seriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.<ref name="weblogo">Crooks GE, Hon G, Chandonia JM, Brenner SE WebLogo: A sequence logo generator,<br />
Genome Research, 14:1188-1190, (2004)</ref>]]<br />
<br />
==== Conformational Changes ====<br />
<br />
Exactly how this structure relates to function is somewhat debated, but it is hypothesized that the fold allows residues preceding the turn to interact with the CVQC motif after the turn. A threonine-7 reside directly across the thioredoxin fold from the disulfide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/17'>"A" conformation</scene>, the alcohol oxygen of the threonine side chain (seen as a red ball) points towards the disulfide bond, forming an electrostatic interaction (represented by a short dashed line) between the two that prevents thioredoxin reductase from binding. Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/16'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space and enough electrostatic freedom for the ligand to bind and reduction to occur.<ref name="Swastik" /><br />
<br />
[[Image:Hydrophobic region pic.png|thumb|right| Hydrophobic region WSGFRP on the surface of MtNrdH (red) bound to ligand (green).<ref name="PyMol">The PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.</ref>]]<br />
<br />
Another highly conserved series of residues is the WSGFRP sequence. This nonpolar sequence is found on the surface of the molecule and is exposed to solvent. For this reason, it has been hypothesized that this sequence plays a role in the binding of thioredoxin reductase. <ref name="Swastik" /><br />
<br />
<scene name='69/694227/Arg_68/4'>Arg-68</scene> is responsible for the stabilization of the hydrophobic region of NrdH. Arg-68 has two distinct conformations. In the <scene name='69/694227/Arg_68_conformation_1/4'>first conformation</scene>, Arg-68 is hydrogen bonded to His- 60 and Asp-59. When Arg-68 shifts to its <scene name='69/694227/Arg_68_conformation_2/5'>second conformation</scene>, it breaks its hydrogen bond with Asp-59. <ref name="Swastik" /> This reduction in hydrogen bonding gives the hydrophobic region more flexibility and is thought to occur when NrdH is in its inactive state. <br />
<br />
[[Image:Wsgfrpweblogo.png|thumb|center|upright=2.5|Weblogo diagram showing highly conserved WSGFRP region of NrdH in four separate protein structures from ''Nocardia seriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.<ref name="weblogo" />]]<br />
<br />
<br />
==== Stabilization ====<br />
The active site of the protein is stabilized through a <scene name='69/696879/Water_coordination/1'>hydrogen bond network</scene> involving the two highly conserved series of residues, CVQC (green) and WSGFRP (yellow). A water molecule appears to be a key part of the H-bonding network. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<ref name="Swastik" /><br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called [http://www.proteopedia.org/wiki/index.php/Ribonucleotide_reductase ribonucleotide reductase (RNR)] to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes.<ref name ="Kolberg">Kolberg, M., et al. (2004) Structure, function, and mechanism of ribonucleotide reductases. Biochim. Biophys. Acta 1699 (1−2), 1−34.</ref> Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thioredoxin, which are first reduced by glutadoxin reductase and thioredoxin reductase, respectively.<ref>Nelson, David L., and Michael M. Cox. Lehninger Principles of Biochemistry. 5th ed. New York: W.H. Freeman, 2008. 888-889.</ref> In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <ref name="Kolberg" /><br />
<br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|Ribonucleotide Reduction Class Ib general mechanism.<ref>Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref> The role of NrdH is highlighted.]] <br />
<br />
== Relevance ==<br />
<br />
Like most NrdHs, MtNrdH is similar in sequence to glutaredoxins, but structurally similar to thioredoxins. MtNrdH also accepts electrons from thioredoxin reductase, a characteristic of thioredoxins, but not glutaredoxins.<ref name="Swastik" /> [[Image:Image-Super imposed molecules.png|thumb|left|Structural comparison of NrdHs with "thioredoxin folds": ''E. Coli'' NrdH (green), ''C. ammoniagenes'' NrdH (blue), ''M. tuberculosis'' NrdH (red)<ref name="PyMol" />]] <br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', ''S. dysenteriae'', and ''C. glutamicium''<ref>Wang, M. et al. Mol Cell Proteomics 2012, doi:10.1074/mcp.O111.014704. http://pax-db.org/#!search?q=NrdH%250A</ref> <ref>Si, M.-R., Zhang, L., Yang, Z.-F., Xu, Y.-X., Liu, Y.-B., Jiang, C.-Y., … Liu, S.-J. (2014). NrdH Redoxin Enhances Resistance to Multiple Oxidative Stresses by Acting as a Peroxidase Cofactor in Corynebacterium glutamicum. Applied and Environmental Microbiology, 80(5), 1750–1762. doi:10.1128/AEM.03654-13</ref> In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or thioredoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. <ref name="Swastik" /> If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
==Possible Drug Target==<br />
<br />
MtNrdH can serve as a potential drug target to treat tuberculosis. The genes encoding NrdE and NrdF2, a cofactor in class 1b ribonucleotide reduction, are essential for growth of M. tuberculosis in vitro.<ref>Mowa, M. B., et al. (2009) Function and regulation of class I ribonucleotide reductase-encoding genes in mycobacteria. J. Bacteriol. 191 (3), 985−995</ref> This suggest that M. tuberculosis relies solely on class Ib ribonucleotide reduction. If that is the case, NrdH may be an essential gene as well. Since NrdH is not found in humans, a drug that targets NrdH would be able to damage M. tuberculosis cells without hurting the human host.<br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2396242Sandbox Reserved 10612015-04-22T00:19:51Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='300' side='right' caption='Micobacterium tuberculosis NrdH' scene='69/694228/Mtnrdh/2'><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH (MtNrdH) is a small glutaredoxin-like protein involved in the electron transport chain in ribonucleotide reduction. Therefore, it is extremely important in DNA production and replication because it helps supply cells with deoxyribonucleotides. Reduction of MtNrdH results in the breaking of an internal disulfide bond at the active site, allowing it to accept electrons and pass them on downstream. Because of its imperative role in ribionucleotide reduction, MtNrdH is thought to be essential to the reproductive integrity of ''M. tuberculosis'', suggesting its role in infectivity and leading to its identification as a possible drug target.<ref name ="Swastik">Swastik, Phulera and Mande, Shekhar C. (2013) The Crystal Structure of Mycobacterium tuberculosis NrdH at 0.87Å Suggests a Possible Mode of Its Activity. Biochemistry 52, 4056-4065.</ref><br />
<br />
== Background ==<br />
<br />
[http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis'']resides in the lungs of a host and upon becoming active, results in a Tuberculosis infection (TB) and the ensuing symptoms of chest pain, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013).<ref name="WHO">"Tuberculosis." Media Centre. World Health Organization, Web. 16 Mar. 2015. Media Centre. <http://www.who.int/mediacentre/factsheets/fs104/en/>.</ref> The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. TB is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative.<ref name="WHO" /><br />
<br />
<br />
== Structure == <br />
<br />
The <scene name='69/694228/Nrdh_structure/1'>MtNrdH structure</scene> determined by x-ray crystallography has 79 residues in a single polypeptide chain. The active site (shown in green) is dominated by a <scene name='69/694228/Nrdh_structure/3'>disulfide bond</scene> between Cys-11 and Cys-14, which serves as the site of reduction by thioredoxin reductase. <ref name="Swastik" /><br />
<br />
Many thioredoxin-like proteins have a similar active site region, which includes the <scene name='69/694228/Nrdh_structure/4'>thioredoxin fold</scene>, a large turn in the protein structure right before the disulfide bond. The residues directly following the fold, <scene name='69/694228/Nrdh_structure/5'>CVQC</scene>, are the most highly conserved of all areas of the protein across multiple species. <br />
[[Image:Weblogocvqc.png|thumb|center|upright=2.5|Weblogo diagram showing highly conserved CVQC region of NrdH in five separate protein structures from ''Nocardiaseriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.<ref name="weblogo">Crooks GE, Hon G, Chandonia JM, Brenner SE WebLogo: A sequence logo generator,<br />
Genome Research, 14:1188-1190, (2004)</ref>]]<br />
<br />
==== Conformational Changes ====<br />
<br />
Exactly how this structure relates to function is somewhat debated, but it is hypothesized that the fold allows residues preceding the turn to interact with the CVQC motif after the turn. A threonine-7 reside directly across the thioredoxin fold from the disulfide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/17'>"A" conformation</scene>, the alcohol oxygen of the threonine side chain (seen as a red ball) points towards the disulfide bond, engaging a electrostatic interaction (represented by a short dashed line) between the two that prevents thioredoxin reductase from binding. Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/16'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space and enough electrostatic freedom for the ligand to bind and reduction to occur.<ref name="Swastik" /><br />
<br />
Another highly conserved series of residues is the WSGFRP sequence. This nonpolar sequence is found on the surface of the molecule and is exposed to solvent. [[Image:Hydrophobic region pic.png|thumb| Hydrophobic region WSGFRP on the surface of MtNrdH (red) bound to ligand (green).<ref name="PyMol">The PyMOL Molecular Graphics System, Version 1.7.4 Schrödinger, LLC.</ref>]] For this reason, it has been hypothesized that this sequence plays a role in the binding of thioredoxin reductase. <ref name="Swastik" />[[Image:Wsgfrpweblogo.png|thumb|center|upright=2.5|Weblogo diagram showing highly conserved WSGFRP region of NrdH in five separate protein structures from ''Nocardiaseriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.<ref name="weblogo" />]]<br />
<br />
<scene name='69/694227/Arg_68/4'>Arg-68</scene> is responsible for the stabilization of the hydrophobic region of NrdH. Arg-68 has two distinct conformations. In the <scene name='69/694227/Arg_68_conformation_1/4'>first conformation</scene>, Arg-68 is hydrogen bonded to His- 60 and Asp-59. When Arg-68 shifts to its <scene name='69/694227/Arg_68_conformation_2/5'>second conformation</scene>, it breaks its hydrogen bond with Asp-59. <ref name="Swastik" /> This reduction in hydrogen bonding gives the hydrophobic region more flexibility and is thought to occur when NrdH is in its inactive state. <br />
<br />
==== Stabilization ====<br />
The active site of the protein is stabilized through a <scene name='69/696879/Water_coordination/1'>hydrogen bond network</scene> involving the two highly conserved series of residues, CVQC (green) and WSGFRP (yellow). The crystal structure shows that interactions with one water molecule is necessary for the proper coordination between the conserved residues to occur. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<ref name="Swastik" /><br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called [http://www.proteopedia.org/wiki/index.php/Ribonucleotide_reductase ribonucleotide reductase (RNR)] to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes.<ref name ="Kolberg">Kolberg, M., et al. (2004) Structure, function, and mechanism of ribonucleotide reductases. Biochim. Biophys. Acta 1699 (1−2), 1−34.</ref> Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thioredoxin, which are first reduced by glutadoxin reductase and thioredoxin reductase, respectively.<ref>Nelson, David L., and Michael M. Cox. Lehninger Principles of Biochemistry. 5th ed. New York: W.H. Freeman, 2008. 888-889.</ref> In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <ref name="Kolberg" /><br />
<br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|Ribonucleotide Reduction Class Ib general mechanism.<ref>Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref> The role of NrdH is highlighted.]] <br />
<br />
== Relevance ==<br />
<br />
Like most NrdHs, MtNrdH is similar in sequence to glutaredoxins, but structurally similar to thioredoxins. MtNrdH also accepts electrons from thioredoxin reductase, a characteristic of thioredoxins, but not glutaredoxins.<ref name="Swastik" /> [[Image:Image-Super imposed molecules.png|thumb|left|Structural comparison of NrdHs with "thioredoxin folds": ''E. Coli'' NrdH (green), ''C. ammoniagenes'' NrdH (blue), ''M. tuberculosis'' NrdH (red)<ref name="PyMol" />]] <br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', and ''S. dysenteriae''. In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or thioredoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. <ref name="Swastik" /> If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
==Possible Drug Target==<br />
<br />
MtNrdH can serve as a potential drug target to treat tuberculosis. The genes encoding NrdE and NrdF2, a cofactor in class 1b ribonucleotide reduction, are essential for growth of M. tuberculosis in vitro.<ref>Mowa, M. B., et al. (2009) Function and regulation of class I ribonucleotide reductase-encoding genes in mycobacteria. J. Bacteriol. 191 (3), 985−995</ref> This suggest that M. tuberculosis relies solely on class Ib ribonucleotide reduction. If that is the case, NrdH may be an essential gene as well. Since NrdH is not found in humans, a drug that targets NrdH would be able to damage M. tuberculosis cells without hurting the human host.<br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2396241Sandbox Reserved 10612015-04-22T00:15:42Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='300' side='right' caption='Micobacterium tuberculosis NrdH' scene='69/694228/Mtnrdh/2'><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH (MtNrdH) is a small glutaredoxin-like protein involved in the electron transport chain in ribonucleotide reduction. Therefore, it is extremely important in DNA production and replication because it helps supply cells with deoxyribonucleotides. Reduction of MtNrdH results in the breaking of an internal disulfide bond at the active site, allowing it to accept electrons and pass them on downstream. Because of its imperative role in ribionucleotide reduction, MtNrdH is thought to be essential to the reproductive integrity of ''M. tuberculosis'', suggesting its role in infectivity and leading to its identification as a possible drug target.<ref name ="Swastik">Swastik, Phulera and Mande, Shekhar C. (2013) The Crystal Structure of Mycobacterium tuberculosis NrdH at 0.87Å Suggests a Possible Mode of Its Activity. Biochemistry 52, 4056-4065.</ref><br />
<br />
== Background ==<br />
<br />
[http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis'']resides in the lungs of a host and upon becoming active, results in a Tuberculosis infection (TB) and the ensuing symptoms of chest pain, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013).<ref name="WHO">"Tuberculosis." Media Centre. World Health Organization, Web. 16 Mar. 2015. Media Centre. <http://www.who.int/mediacentre/factsheets/fs104/en/>.</ref> The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. TB is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative.<ref name="WHO" /><br />
<br />
<br />
== Structure == <br />
<br />
The <scene name='69/694228/Nrdh_structure/1'>MtNrdH structure</scene> determined by x-ray crystallography has 79 residues in a single polypeptide chain. The active site (shown in green) is dominated by a <scene name='69/694228/Nrdh_structure/3'>disulfide bond</scene> between Cys-11 and Cys-14, which serves as the site of reduction by thioredoxin reductase. <ref name="Swastik" /><br />
<br />
Many thioredoxin-like proteins have a similar active site region, which includes the <scene name='69/694228/Nrdh_structure/4'>thioredoxin fold</scene>, a large turn in the protein structure right before the disulfide bond. The residues directly following the fold, <scene name='69/694228/Nrdh_structure/5'>CVQC</scene>, are the most highly conserved of all areas of the protein across multiple species. <br />
[[Image:Weblogocvqc.png|thumb|center|upright=2.5|Weblogo diagram showing highly conserved CVQC region of NrdH in five separate protein structures from ''Nocardiaseriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.<ref name="weblogo">Crooks GE, Hon G, Chandonia JM, Brenner SE WebLogo: A sequence logo generator,<br />
Genome Research, 14:1188-1190, (2004)</ref>]]<br />
<br />
==== Conformational Changes ====<br />
<br />
Exactly how this structure relates to function is somewhat debated, but it is hypothesized that the fold allows residues preceding the turn to interact with the CVQC motif after the turn. A threonine-7 reside directly across the thioredoxin fold from the disulfide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/17'>"A" conformation</scene>, the alcohol oxygen of the threonine side chain (seen as a red ball) points towards the disulfide bond, engaging a electrostatic interaction (represented by a short dashed line) between the two that prevents thioredoxin reductase from binding. Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/16'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space and enough electrostatic freedom for the ligand to bind and reduction to occur.<ref name="Swastik" /><br />
<br />
Another highly conserved series of residues is the WSGFRP sequence. This nonpolar sequence is found on the surface of the molecule and is exposed to solvent. [[Image:Hydrophobic region pic.png|thumb| Hydrophobic region WSGFRP on the surface of MtNrdH (red) bound to ligand (green).<ref name="Hanson">DOI 10.1002/ijch.201300024</ref>]] For this reason, it has been hypothesized that this sequence plays a role in the binding of thioredoxin reductase. <ref name="Swastik" />[[Image:Wsgfrpweblogo.png|thumb|center|upright=2.5|Weblogo diagram showing highly conserved WSGFRP region of NrdH in five separate protein structures from ''Nocardiaseriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.<ref name="weblogo" />]]<br />
<br />
<scene name='69/694227/Arg_68/4'>Arg-68</scene> is responsible for the stabilization of the hydrophobic region of NrdH. Arg-68 has two distinct conformations. In the <scene name='69/694227/Arg_68_conformation_1/4'>first conformation</scene>, Arg-68 is hydrogen bonded to His- 60 and Asp-59. When Arg-68 shifts to its <scene name='69/694227/Arg_68_conformation_2/5'>second conformation</scene>, it breaks its hydrogen bond with Asp-59. <ref name="Swastik" /> This reduction in hydrogen bonding gives the hydrophobic region more flexibility and is thought to occur when NrdH is in its inactive state. <br />
<br />
==== Stabilization ====<br />
The active site of the protein is stabilized through a <scene name='69/696879/Water_coordination/1'>hydrogen bond network</scene> involving the two highly conserved series of residues, CVQC (green) and WSGFRP (yellow). The crystal structure shows that interactions with one water molecule is necessary for the proper coordination between the conserved residues to occur. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<ref name="Swastik" /><br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called [http://www.proteopedia.org/wiki/index.php/Ribonucleotide_reductase ribonucleotide reductase (RNR)] to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes.<ref name ="Kolberg">Kolberg, M., et al. (2004) Structure, function, and mechanism of ribonucleotide reductases. Biochim. Biophys. Acta 1699 (1−2), 1−34.</ref> Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thioredoxin, which are first reduced by glutadoxin reductase and thioredoxin reductase, respectively.<ref>Nelson, David L., and Michael M. Cox. Lehninger Principles of Biochemistry. 5th ed. New York: W.H. Freeman, 2008. 888-889.</ref> In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <ref name="Kolberg" /><br />
<br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|Ribonucleotide Reduction Class Ib general mechanism.<ref>Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref> The role of NrdH is highlighted.]] <br />
<br />
== Relevance ==<br />
<br />
Like most NrdHs, MtNrdH is similar in sequence to glutaredoxins, but structurally similar to thioredoxins. MtNrdH also accepts electrons from thioredoxin reductase, a characteristic of thioredoxins, but not glutaredoxins.<ref name="Swastik" /> [[Image:Image-Super imposed molecules.png|thumb|left|Structural comparison of NrdHs with "thioredoxin folds": ''E. Coli'' NrdH (green), ''C. ammoniagenes'' NrdH (blue), ''M. tuberculosis'' NrdH (red)<ref name="Hanson" />]] <br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', and ''S. dysenteriae''. In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or thioredoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. <ref name="Swastik" /> If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
==Possible Drug Target==<br />
<br />
MtNrdH can serve as a potential drug target to treat tuberculosis. The genes encoding NrdE and NrdF2, a cofactor in class 1b ribonucleotide reduction, are essential for growth of M. tuberculosis in vitro.<ref>Mowa, M. B., et al. (2009) Function and regulation of class I ribonucleotide reductase-encoding genes in mycobacteria. J. Bacteriol. 191 (3), 985−995</ref> This suggest that M. tuberculosis relies solely on class Ib ribonucleotide reduction. If that is the case, NrdH may be an essential gene as well. Since NrdH is not found in humans, a drug that targets NrdH would be able to damage M. tuberculosis cells without hurting the human host.<br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1060&diff=2396240Sandbox Reserved 10602015-04-22T00:14:00Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==Your Heading Here (maybe something like 'Structure')==<br />
<StructureSection load='4hs1' size='340' side='right' caption='Caption for this structure' scene='69/694227/Arg_68/4'><br />
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
<scene name='69/694227/Arg_68_conformation_1/3'>TextToBeDisplayed</scene><br />
<br />
<scene name='69/694227/Arg_68_conformation_1/2'>lets try again</scene><br />
<br />
<scene name='69/694227/Arg_68_conformation_2/1'>Conformation 2</scene><br />
<br />
<scene name='69/694227/Arg_68_conformation_1/4'>Hydrogen bonded</scene><br />
<br />
<scene name='69/694227/Arg_68_conformation_2/5'>Not hydrogen bonded</scene><br />
<br />
<scene name='69/694227/Arg_68/3'>Full molecule scene</scene><br />
<br />
<scene name='69/694227/Arg_68/4'>Full molecule scene with fixed label</scene><br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2396233Sandbox Reserved 10612015-04-21T23:36:50Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='300' side='right' caption='Micobacterium tuberculosis NrdH' scene=''><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH (MtNrdH) is a small glutaredoxin-like protein involved in the electron transport chain in ribonucleotide reduction. Therefore, it is extremely important in DNA production and replication because it helps supply cells with deoxyribonucleotides. Reduction of MtNrdH results in the breaking of an internal disulfide bond at the active site, allowing it to accept electrons and pass them on downstream. Because of its imperative role in ribionucleotide reduction, MtNrdH is thought to be essential to the reproductive integrity of ''M. tuberculosis'', suggesting its role in infectivity and leading to its identification as a possible drug target.<ref name ="Swastik">Swastik, Phulera and Mande, Shekhar C. (2013) The Crystal Structure of Mycobacterium tuberculosis NrdH at 0.87Å Suggests a Possible Mode of Its Activity. Biochemistry 52, 4056-4065.</ref><br />
<br />
== Background ==<br />
<br />
[http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis'']resides in the lungs of a host and upon becoming active, results in a Tuberculosis infection (TB) and the ensuing symptoms of chest pain, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013).<ref name="WHO">"Tuberculosis." Media Centre. World Health Organization, Web. 16 Mar. 2015. Media Centre. <http://www.who.int/mediacentre/factsheets/fs104/en/>.</ref> The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. TB is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative.<ref name="WHO" /><br />
<br />
<br />
== Structure == <br />
<br />
The <scene name='69/694228/Nrdh_structure/1'>MtNrdH structure</scene> determined by x-ray crystallography has 79 residues in a single polypeptide chain. The active site (shown in green) is dominated by a <scene name='69/694228/Nrdh_structure/3'>disulfide bond</scene> between Cys-11 and Cys-14, which serves as the site of reduction by thioredoxin reductase. <ref name="Swastik" /><br />
<br />
Many thioredoxin-like proteins have a similar active site region, which includes the <scene name='69/694228/Nrdh_structure/4'>thioredoxin fold</scene>, a large turn in the protein structure right before the disulfide bond. The residues directly following the fold, <scene name='69/694228/Nrdh_structure/5'>CVQC</scene>, are the most highly conserved of all areas of the protein across multiple species. <br />
[[Image:Weblogocvqc.png|thumb|center|upright=2.5|Weblogo diagram showing highly conserved CVQC region of NrdH in five separate protein structures from ''Nocardiaseriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.]]<br />
<br />
==== Variable Conformations ====<br />
<br />
Exactly how this structure relates to function is somewhat debated, but it is hypothesized that the fold allows residues preceding the turn to interact with the CVQC motif after the turn. A threonine-7 reside directly across the thioredoxin fold from the disulfide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/17'>"A" conformation</scene>, the alcohol oxygen of the threonine side chain (seen as a red ball) points towards the disulfide bond, engaging a electrostatic interaction (represented by a short dashed line) between the two that prevents thioredoxin reductase from binding. Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/16'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space and enough electrostatic freedom for the ligand to bind and reduction to occur.<ref name="Swastik" /><br />
<br />
Another highly conserved series of residues is the WSGFRP sequence. This nonpolar sequence is found on the surface of the molecule and is exposed to solvent. [[Image:Hydrophobic region pic.png|thumb| Hydrophobic region WSGFRP on the surface of MtNrdH (red) bound to ligand (green).<ref name="Hanson">DOI 10.1002/ijch.201300024</ref>]] For this reason, it has been hypothesized that this sequence plays a role in the binding of thioredoxin reductase. <ref name="Swastik" />[[Image:Wsgfrpweblogo.png|thumb|center|upright=2.5|Weblogo diagram showing highly conserved WSGFRP region of NrdH in five separate protein structures from ''Nocardiaseriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.]]<br />
<br />
<scene name='69/694227/Arg_68/4'>Arg-68</scene> is responsible for the stabilization of the hydrophobic region of NrdH. Arg-68 has two distinct conformations. In the <scene name='69/694227/Arg_68_conformation_1/4'>first conformation</scene>, Arg-68 is hydrogen bonded to His- 60 and Asp-59. When Arg-68 shifts to its <scene name='69/694227/Arg_68_conformation_2/5'>second conformation</scene>, it breaks its hydrogen bond with Asp-59. <ref name="Swastik" /> This reduction in hydrogen bonding gives the hydrophobic region more flexibility and is thought to occur when NrdH is in its inactive state. <br />
<br />
==== Stabilization ====<br />
The active site of the protein is stabilized through a <scene name='69/696879/Water_coordination/1'>hydrogen bond network</scene> involving the two highly conserved series of residues, CVQC (green) and WSGFRP (yellow). The crystal structure shows that interactions with one water molecule is necessary for the proper coordination between the conserved residues to occur. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<ref name="Swastik" /><br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called [http://www.proteopedia.org/wiki/index.php/Ribonucleotide_reductase ribonucleotide reductase (RNR)] to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes.<ref name ="Kolberg">Kolberg, M., et al. (2004) Structure, function, and mechanism of ribonucleotide reductases. Biochim. Biophys. Acta 1699 (1−2), 1−34.</ref> Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thioredoxin, which are first reduced by glutadoxin reductase and thioredoxin reductase, respectively.<ref>Nelson, David L., and Michael M. Cox. Lehninger Principles of Biochemistry. 5th ed. New York: W.H. Freeman, 2008. 888-889.</ref> In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <ref name="Kolberg" /><br />
<br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|Ribonucleotide Reduction Class Ib general mechanism.<ref>Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref> The role of NrdH is highlighted.]] <br />
<br />
== Relevance ==<br />
<br />
Like most NrdHs, MtNrdH is similar in sequence to glutaredoxins, but structurally similar to thioredoxins. MtNrdH also accepts electrons from thioredoxin reductase, a characteristic of thioredoxins, but not glutaredoxins.<ref name="Swastik" /> [[Image:Image-Super imposed molecules.png|thumb|left|Structural comparison of NrdHs with "thioredoxin folds": ''E. Coli'' NrdH (green), ''C. ammoniagenes'' NrdH (blue), ''M. tuberculosis'' NrdH (red)<ref name="Hanson" />]] <br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', and ''S. dysenteriae''. In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or thioredoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. <ref name="Swastik" /> If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
==Possible Drug Target==<br />
<br />
MtNrdH can serve as a potential drug target to treat tuberculosis. The genes encoding NrdE and NrdF2, a cofactor in class 1b ribonucleotide reduction, are essential for growth of M. tuberculosis in vitro.<ref>Mowa, M. B., et al. (2009) Function and regulation of class I ribonucleotide reductase-encoding genes in mycobacteria. J. Bacteriol. 191 (3), 985−995</ref> This suggest that M. tuberculosis relies solely on class Ib ribonucleotide reduction. If that is the case, NrdH may be an essential gene as well. Since NrdH is not found in humans, a drug that targets NrdH would be able to damage M. tuberculosis cells without hurting the human host.<br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2396229Sandbox Reserved 10612015-04-21T23:28:01Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='300' side='right' caption='Micobacterium tuberculosis NrdH' scene=''><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH (MtNrdH) is a small glutaredoxin-like protein involved in the electron transport chain in ribonucleotide reduction. Therefore, it is extremely important in DNA production and replication because it helps supply cells with deoxyribonucleotides. Reduction of MtNrdH results in the breaking of an internal disulfide bond at the active site, allowing it to accept electrons and pass them on downstream. Because of its imperative role in ribionucleotide reduction, MtNrdH is thought to be essential to the reproductive integrity of ''M. tuberculosis'', suggesting its role in infectivity and leading to its identification as a possible drug target.<ref name ="Swastik">Swastik, Phulera and Mande, Shekhar C. (2013) The Crystal Structure of Mycobacterium tuberculosis NrdH at 0.87Å Suggests a Possible Mode of Its Activity. Biochemistry 52, 4056-4065.</ref><br />
<br />
== Background ==<br />
<br />
[http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis'']resides in the lungs of a host and upon becoming active, results in a Tuberculosis infection (TB) and the ensuing symptoms of chest pain, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013).<ref name="WHO">"Tuberculosis." Media Centre. World Health Organization, Web. 16 Mar. 2015. Media Centre. <http://www.who.int/mediacentre/factsheets/fs104/en/>.</ref> The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. TB is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative.<ref name="WHO" /><br />
<br />
<br />
== Structure == <br />
<br />
The <scene name='69/694228/Nrdh_structure/1'>MtNrdH structure</scene> determined by x-ray crystallography has 79 residues in a single polypeptide chain. The active site (shown in green) is dominated by a <scene name='69/694228/Nrdh_structure/3'>disulfide bond</scene> between Cys-11 and Cys-14, which serves as the site of reduction by thioredoxin reductase. <ref name="Swastik" /><br />
<br />
Many thioredoxin-like proteins have a similar active site region, which includes the <scene name='69/694228/Nrdh_structure/4'>thioredoxin fold</scene>, a large turn in the protein structure right before the disulfide bond. The residues directly following the fold, <scene name='69/694228/Nrdh_structure/5'>CVQC</scene>, are the most highly conserved of all areas of the protein across multiple species. <br />
[[Image:Weblogocvqc.png|thumb|center|upright=2.5|Weblogo diagram showing highly conserved CVQC region of NrdH in five separate protein structures from ''Nocardiaseriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.]]<br />
<br />
==== Variable Conformations ====<br />
<br />
Exactly how this structure relates to function is somewhat debated, but it is hypothesized that the fold allows residues preceding the turn to interact with the CVQC motif after the turn. A threonine-7 reside directly across the thioredoxin fold from the disulfide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/17'>"A" conformation</scene>, the alcohol oxygen of the threonine side chain (seen as a red ball) points towards the disulfide bond, engaging a electrostatic interaction (represented by a short dashed line) between the two that prevents thioredoxin reductase from binding. Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/16'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space and enough electrostatic freedom for the ligand to bind and reduction to occur.<ref name="Swastik" /><br />
<br />
Another highly conserved series of residues is the WSGFRP sequence. This nonpolar sequence is found on the surface of the molecule and is exposed to solvent. [[Image:Hydrophobic region pic.png|thumb| Hydrophobic region WSGFRP on the surface of MtNrdH (red) bound to ligand (green).]]<ref>DOI 10.1002/ijch.201300024</ref> <ref>PMID:21638687</ref> For this reason, it has been hypothesized that this sequence plays a role in the binding of thioredoxin reductase. <ref name="Swastik" />[[Image:Wsgfrpweblogo.png|thumb|center|upright=2.5|Weblogo diagram showing highly conserved WSGFRP region of NrdH in five separate protein structures from ''Nocardiaseriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.]]<br />
<br />
<scene name='69/694227/Arg_68/4'>Arg-68</scene> is responsible for the stabilization of the hydrophobic region of NrdH. Arg-68 has two distinct conformations. In the <scene name='69/694227/Arg_68_conformation_1/4'>first conformation</scene>, Arg-68 is hydrogen bonded to His- 60 and Asp-59. When Arg-68 shifts to its <scene name='69/694227/Arg_68_conformation_2/5'>second conformation</scene>, it breaks its hydrogen bond with Asp-59. <ref name="Swastik" /> This reduction in hydrogen bonding gives the hydrophobic region more flexibility and is thought to occur when NrdH is in its inactive state. <br />
<br />
==== Stabilization ====<br />
The active site of the protein is stabilized through a <scene name='69/696879/Water_coordination/1'>hydrogen bond network</scene> involving the two highly conserved series of residues, CVQC (green) and WSGFRP (yellow). The crystal structure shows that interactions with one water molecule is necessary for the proper coordination between the conserved residues to occur. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<ref name="Swastik" /><br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called [http://www.proteopedia.org/wiki/index.php/Ribonucleotide_reductase ribonucleotide reductase (RNR)] to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes.<ref name ="Kolberg">Kolberg, M., et al. (2004) Structure, function, and mechanism of ribonucleotide reductases. Biochim. Biophys. Acta 1699 (1−2), 1−34.</ref> Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thioredoxin, which are first reduced by glutadoxin reductase and thioredoxin reductase, respectively.<ref>Nelson, David L., and Michael M. Cox. Lehninger Principles of Biochemistry. 5th ed. New York: W.H. Freeman, 2008. 888-889.</ref> In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <ref name="Kolberg" /><br />
<br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|Ribonucleotide Reduction Class Ib general mechanism.<ref>Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref> The role of NrdH is highlighted.]] <br />
<br />
== Relevance ==<br />
<br />
Like most NrdHs, MtNrdH is similar in sequence to glutaredoxins, but structurally similar to thioredoxins. MtNrdH also accepts electrons from thioredoxin reductase, a characteristic of thioredoxins, but not glutaredoxins.<ref name="Swastik" /> [[Image:Image-Super imposed molecules.png|thumb|left|Structural comparison of NrdHs with "thioredoxin folds": ''E. Coli'' NrdH (green), ''C. ammoniagenes'' NrdH (blue), ''M. tuberculosis'' NrdH (red)]]<ref>DOI 10.1002/ijch.201300024</ref> <ref>PMID:21638687</ref> <br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', and ''S. dysenteriae''. In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or thioredoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. <ref name="Swastik" /> If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
==Possible Drug Target==<br />
<br />
MtNrdH can serve as a potential drug target to treat tuberculosis. The genes encoding NrdE and NrdF2, a cofactor in class 1b ribonucleotide reduction, are essential for growth of M. tuberculosis in vitro.<ref name="Swastik" /> This suggest that M. tuberculosis relies solely on class Ib ribonucleotide reduction. If that is the case, NrdH may be an essential gene as well. Since NrdH is not found in humans, a drug that targets NrdH would be able to damage M. tuberculosis cells without hurting the human host.<br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2396225Sandbox Reserved 10612015-04-21T23:14:54Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='300' side='right' caption='Micobacterium tuberculosis NrdH' scene=''><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH (MtNrdH) is a small glutaredoxin-like protein involved in the electron transport chain in ribonucleotide reduction. Therefore, it is extremely important in DNA production and replication because it helps supply cells with deoxyribonucleotides. Reduction of MtNrdH results in the breaking of an internal disulfide bond at the active site, allowing it to accept electrons and pass them on downstream. Because of its imperative role in ribionucleotide reduction, MtNrdH is thought to be essential to the reproductive integrity of ''M. tuberculosis'', suggesting its role in infectivity and leading to its identification as a possible drug target.<ref name ="Swastik">Swastik, Phulera and Mande, Shekhar C. (2013) The Crystal Structure of Mycobacterium tuberculosis NrdH at 0.87Å Suggests a Possible Mode of Its Activity. Biochemistry 52, 4056-4065.</ref><br />
<br />
== Background ==<br />
<br />
[http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis ''Mycobacterium tuberculosis'']resides in the lungs of a host and upon becoming active, results in a Tuberculosis infection (TB) and the ensuing symptoms of chest pain, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013).<ref name="WHO">"Tuberculosis." Media Centre. World Health Organization, Web. 16 Mar. 2015. Media Centre. <http://www.who.int/mediacentre/factsheets/fs104/en/>.</ref> The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. TB is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative.<ref name="WHO" /><br />
<br />
<br />
== Structure == <br />
<br />
The <scene name='69/694228/Nrdh_structure/1'>MtNrdH structure</scene> determined by x-ray crystallography has 79 residues in a single polypeptide chain. The active site (shown in green) is dominated by a <scene name='69/694228/Nrdh_structure/3'>disulfide bond</scene> between Cys-11 and Cys-14, which serves as the site of reduction by thioredoxin reductase. <ref name="Swastik" /><br />
<br />
Many thioredoxin-like proteins have a similar active site region, which includes the <scene name='69/694228/Nrdh_structure/4'>thioredoxin fold</scene>, a large turn in the protein structure right before the disulfide bond. The residues directly following the fold, <scene name='69/694228/Nrdh_structure/5'>CVQC</scene>, are the most highly conserved of all areas of the protein across multiple species. <br />
[[Image:Weblogocvqc.png|thumb|center|upright=2.5|Weblogo diagram showing highly conserved CVQC region of NrdH in five separate protein structures from ''Nocardiaseriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.]]<br />
<br />
==== Variable Conformations ====<br />
<br />
Exactly how this structure relates to function is somewhat debated, but it is hypothesized that the fold allows residues preceding the turn to interact with the CVQC motif after the turn. A threonine-7 reside directly across the thioredoxin fold from the disulfide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/17'>"A" conformation</scene>, the alcohol oxygen of the threonine side chain (seen as a red ball) points towards the disulfide bond, engaging a electrostatic interaction (represented by a short dashed line) between the two that prevents thioredoxin reductase from binding. Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/16'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space and enough electrostatic freedom for the ligand to bind and reduction to occur.<ref name="Swastik" /><br />
<br />
Another highly conserved series of residues is the WSGFRP sequence. This nonpolar sequence is found on the surface of the molecule and is exposed to solvent. [[Image:Hydrophobic region pic.png|thumb| Hydrophobic region WSGFRP on the surface of MtNrdH (red) bound to ligand (green).]]<ref>DOI 10.1002/ijch.201300024</ref> <ref>PMID:21638687</ref> For this reason, it has been hypothesized that this sequence plays a role in the binding of thioredoxin reductase. <ref name="Swastik" />[[Image:Wsgfrpweblogo.png|thumb|center|upright=2.5|Weblogo diagram showing highly conserved WSGFRP region of NrdH in five separate protein structures from ''Nocardiaseriolae'', ''E. coli'', ''Cornebacterium Ammoniagenes'', and ''Mycobacterium Tuberculosis''.]]<br />
<br />
<scene name='69/694227/Arg_68/4'>Arg-68</scene> is responsible for the stabilization of the hydrophobic region of NrdH. Arg-68 has two distinct conformations. In the <scene name='69/694227/Arg_68_conformation_1/4'>first conformation</scene>, Arg-68 is hydrogen bonded to His- 60 and Asp-59. When Arg-68 shifts to its <scene name='69/694227/Arg_68_conformation_2/5'>second conformation</scene>, it breaks its hydrogen bond with Asp-59. <ref name="Swastik" /> This reduction in hydrogen bonding gives the hydrophobic region more flexibility and is thought to occur when NrdH is in its inactive state. <br />
<br />
==== Stabilization ====<br />
The active site of the protein is stabilized through a <scene name='69/696879/Water_coordination/1'>hydrogen bond network</scene> involving the two highly conserved series of residues, CVQC (green) and WSGFRP (yellow). The crystal structure shows that interactions with one water molecule is necessary for the proper coordination between the conserved residues to occur. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<ref name="Swastik" /><br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called [http://www.proteopedia.org/wiki/index.php/Ribonucleotide_reductase ribonucleotide reductase (RNR)] to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes.<ref name="Swastik" /> Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thioredoxin, which are first reduced by glutadoxin reductase and thioredoxin reductase, respectively.<ref>Nelson, David L., and Michael M. Cox. Lehninger Principles of Biochemistry. 5th ed. New York: W.H. Freeman, 2008. 888-889.</ref> In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <ref name="Swastik" /><br />
<br />
<ref>Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref><br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|Ribonucleotide Reduction Class Ib general mechanism. The role of NrdH is highlighted.]] <br />
<br />
== Relevance ==<br />
<br />
Like most NrdHs, MtNrdH is similar in sequence to glutaredoxins, but structurally similar to thioredoxins. MtNrdH also accepts electrons from thioredoxin reductase, a characteristic of thioredoxins, but not glutaredoxins.<ref name="Swastik" /> [[Image:Image-Super imposed molecules.png|thumb|left|Structural comparison of NrdHs with "thioredoxin folds": ''E. Coli'' NrdH (green), ''C. ammoniagenes'' NrdH (blue), ''M. tuberculosis'' NrdH (red)]]<ref>DOI 10.1002/ijch.201300024</ref> <ref>PMID:21638687</ref> <br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', and ''S. dysenteriae''. In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or thioredoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. <ref name="Swastik" /> If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
==Possible Drug Target==<br />
<br />
MtNrdH can serve as a potential drug target to treat tuberculosis. The genes encoding NrdE and NrdF2, a cofactor in class 1b ribonucleotide reduction, are essential for growth of M. tuberculosis in vitro.<ref name="Swastik" /> This suggest that M. tuberculosis relies solely on class Ib ribonucleotide reduction. If that is the case, NrdH may be an essential gene as well. Since NrdH is not found in humans, a drug that targets NrdH would be able to damage M. tuberculosis cells without hurting the human host.<br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1060&diff=2396224Sandbox Reserved 10602015-04-21T23:08:50Z<p>Katelyn Burke: </p>
<hr />
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==Your Heading Here (maybe something like 'Structure')==<br />
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
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<scene name='69/694227/Arg_68_conformation_1/3'>TextToBeDisplayed</scene><br />
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== Function ==<br />
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== Structural highlights ==<br />
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This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1060&diff=2396223Sandbox Reserved 10602015-04-21T23:03:29Z<p>Katelyn Burke: </p>
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==Your Heading Here (maybe something like 'Structure')==<br />
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<scene name='69/694227/Arg_68_conformation_1/4'>Hydrogen bonded</scene><br />
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<scene name='69/694227/Arg_68_conformation_2/5'>Not hydrogen bonded</scene><br />
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<scene name='69/694227/Arg_68/3'>Full molecule scene</scene><br />
== Function ==<br />
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== Disease ==<br />
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== Relevance ==<br />
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== Structural highlights ==<br />
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This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1060&diff=2395776Sandbox Reserved 10602015-04-17T18:26:09Z<p>Katelyn Burke: </p>
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==Your Heading Here (maybe something like 'Structure')==<br />
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<scene name='69/694227/Arg_68_conformation_2/5'>Not hydrogen bonded</scene><br />
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== Function ==<br />
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== Relevance ==<br />
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== Structural highlights ==<br />
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This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
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</StructureSection><br />
== References ==<br />
<references/></div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1060&diff=2395770Sandbox Reserved 10602015-04-17T18:18:33Z<p>Katelyn Burke: </p>
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==Your Heading Here (maybe something like 'Structure')==<br />
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<scene name='69/694227/Arg_68_conformation_1/4'>This one should look pretty</scene><br />
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== Function ==<br />
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== Disease ==<br />
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== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2393937Sandbox Reserved 10612015-04-11T02:41:42Z<p>Katelyn Burke: </p>
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== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='300' side='right' caption='Micobacterium tuberculosis NrdH' scene=''><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH is a small glutaredoxin-like protein involved in the electron transport chain in ribonucleotide reduction. Therefore, it is extremely important in DNA production and replication because it helps supply cells with deoxyribonucleotides. Reduction of MtNrdH results in the breaking of an internal disulfide bond at the active site, allowing it to accept electrons and pass them on downstream <ref>Swastik, Phulera and Mande, Shekhar C. (2013) The Crystal Structure of Mycobacterium tuberculosis NrdH at 0.87Å Suggests a Possible Mode of Its Activity. Biochemistry 52, 4056-4065.</ref><br />
<br />
== Background ==<br />
<br />
''Mycobacterium tuberculosis'' [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Wikipedia]resides in the lungs of a host and upon becoming active, results in symptoms such as chest pains, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013).<ref>"Tuberculosis." Media Centre. World Health Organization, Web. 16 Mar. 2015. Media Centre. <http://www.who.int/mediacentre/factsheets/fs104/en/>.</ref>The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. Tuberculosis is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative. <ref>"Tuberculosis." Media Centre. World Health Organization, Web. 16 Mar. 2015. Media Centre. <http://www.who.int/mediacentre/factsheets/fs104/en/>.</ref><br />
<br />
<br />
<br />
== Structure == <br />
<br />
The structure of ''M. tuberculosis'' as determined by x-ray crystallography has 79 residues in a single polypeptide chain. <scene name='69/694228/Nrdh_structure/1'>NrdH Chrystal Structure</scene>. The active site (shown in green) is dominated by a disulfide bond between Cys-11 and Cys-14, which serves as the site of reduction by theirodoxin reductase. <ref>Swastik, Phulera and Mande, Shekhar C. (2013) The Crystal Structure of Mycobacterium tuberculosis NrdH at 0.87Å Suggests a Possible Mode of Its Activity. Biochemistry 52, 4056-4065.</ref><br />
<br />
Many thioredoxin-like proteins have a similar active site region, denoted as the thioredoxin fold, which occurs directly before the disulfide bond. The residues in this region, denoted by letters CVQC, are the most highly conserved of all areas of the protein across multiple species. Exactly how this structure relates to function is somewhat debated. A threonine-7 reside directly across the thioredoxin fold from the disulfide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/8'>"A" Conformation</scene>, the alcohol of the threonine side chain points towards the disulfide bond, engaging an ionic interaction between the two that prevents thioredoxin reductase from binding. Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/12'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space for the ligand to bind and reduction to occur.<ref>Swastik, Phulera and Mande, Shekhar C. (2013) The Crystal Structure of Mycobacterium tuberculosis NrdH at 0.87Å Suggests a Possible Mode of Its Activity. Biochemistry 52, 4056-4065.</ref><br />
<br />
The active site of the protein is stabilized through a <scene name='69/696879/Water_coordination/1'>hydrogen bond network</scene> involving the two highly conserved residues, CVQC (green) and [http://www.proteopedia.org/wiki/index.php/Image:Weblogowsgfrp.png WSGFRP] (yellow). The crystal structure shows that interactions with one water molecule is necessary for the proper coordination between the conserved motifs to occur. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<ref>Swastik, Phulera and Mande, Shekhar C. (2013) The Crystal Structure of Mycobacterium tuberculosis NrdH at 0.87Å Suggests a Possible Mode of Its Activity. Biochemistry 52, 4056-4065.</ref><br />
<br />
[[Image:Weblogocvqc.png|thumb|center|upright=2.5|Weblogo diagram showing highly conserved CVQC region of NrdH.]]<br />
<br />
Another highly conserved residue is the WSGFRP sequence. This nonpolar sequence is found on the surface of the molecule and is exposed to solvent. [[Image:Hydrophobic region pic.png|thumb| Hydrophobic region WSGFRP on the surface of MtNrdH (red) bound to ligand (green).]]<ref>DOI 10.1002/ijch.201300024</ref> <ref>PMID:21638687</ref> For this reason, it has been hypothesized that this sequence plays a role in the binding of thioredoxin reductase. <ref>Swastik, Phulera and Mande, Shekhar C. (2013) 4060.</ref> <br />
Arg-68 is responsible for the stabilization of the hydrophobic region of NrdH. Arg-68 has two distinct conformations. In the <scene name='69/694227/Arg_68_conformation_1/3'>first conformation</scene>, Arg-68 is hydrogen bonded to His- 60 and Asp-59. When Arg-68 shifts to its <scene name='69/694227/Arg_68_conformation_2/2'>second conformation</scene><br />
, it breaks its hydrogen bond with Asp-59. <ref>Swastik, Phulera and Mande, Shekhar C. (2013) 4057.</ref> This reduction in hydrogen bonding gives the hydrophobic region more flexibility and is thought to occur when NrdH is in its inactive state. <br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called [http://www.proteopedia.org/wiki/index.php/Ribonucleotide_reductase ribonucleotide reductase (RNR)] to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes.<ref>Swastik, Phulera and Mande, Shekhar C. (2013) 4056.</ref> Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thioredoxin, which are first reduced by glutadoxin reductase and thioredoxin reductase, respectively.<ref>Nelson, David L., and Michael M. Cox. Lehninger Principles of Biochemistry. 5th ed. New York: W.H. Freeman, 2008. 888-889.</ref> In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <ref>Swastik, Phulera and Mande, Shekhar C. (2013) 4056.</ref> <br />
<br />
<ref>Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref><br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|Ribonucleotide Reduction Class Ib general mechanism. The role of NrdH is highlighted.]] <br />
<br />
== Relevance ==<br />
<br />
Like most NrdHs, MtNrdH is similar in sequence to glutaredoxins, but structurally similar to thioredoxins. MtNrdH also accepts electrons from thioredoxin reductase, a characteristic of thioredoxins, but not glutaredoxins.<ref>Swastik, Phulera and Mande, Shekhar C. (2013) 4057.</ref> [[Image:Image-Super imposed molecules.png|thumb|left|Structural comparison of NrdHs with "thioredoxin folds": ''E. Coli'' NrdH (green), ''C. ammoniagenes'' NrdH (blue), ''M. tuberculosis'' NrdH (red)]]<ref>DOI 10.1002/ijch.201300024</ref> <ref>PMID:21638687</ref> <br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', and ''S. dysenteriae''. In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or thioredoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. <ref>Swastik, Phulera and Mande, Shekhar C. (2013) The Crystal Structure of Mycobacterium tuberculosis NrdH at 0.87Å Suggests a Possible Mode of Its Activity. Biochemistry 52, 4056-4065.</ref> If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
==Possible Drug Target==<br />
<br />
MtNrdH can serve as a potential drug target to treat tuberculosis. The genes encoding NrdE and NrdF2, a cofactor in class 1b ribonucleotide reduction, are essential for growth of M. tuberculosis in vitro.<ref>Swastik, Phulera and Mande, Shekhar C. (2013) 4057.</ref> This suggest that M. tuberculosis relies solely on class Ib ribonucleotide reduction. If that is the case, NrdH may be an essential gene as well. Since NrdH is not found in humans, a drug that targets NrdH would be able to damage M. tuberculosis cells without hurting the human host.<br />
<br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2393816Sandbox Reserved 10612015-04-10T17:07:48Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='300' side='right' caption='Micobacterium tuberculosis NrdH' scene=''><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH is a small glutaredoxin-like protein involved in the electron transport chain in ribonucleotide reduction.<ref>Swastik, Phulera and Mande, Shekhar C. (2013) The Crystal Structure of Mycobacterium tuberculosis NrdH at 0.87Å Suggests a Possible Mode of Its Activity. Biochemistry 52, 4056-4065.</ref><br />
<br />
== Background ==<br />
<br />
''Mycobacterium tuberculosis'' [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Wikipedia]resides in the lungs of a host and upon becoming active, results in symptoms such as chest pains, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013). The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. Tuberculosis is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative. <br />
<br />
<br />
== Structure == <br />
<br />
The structure of ''M. tuberculosis'' as determined by x-ray crystallography has 79 residues in a single polypeptide chain. <scene name='69/694228/Nrdh_structure/1'>NrdH Chrystal Structure</scene>. The active site (shown in green) is dominated by a disulphide bond between Cys-11 and Cys-14, which serves as the site of reduction by Theirodoxin reductase. <br />
<br />
Many theirodoxin-like proteins have a similar active site region, denoted as the theirodoxin fold, which occurs directly before the disulfide bond. The residues in this region, denoted by letters CVQC, are the most highly conserved of all areas of the protein across multiple species. Exactly how this structure relates to function is somewhat debated. A Threonine-7 reside directly across the theirodoxin fold from the disulphide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the Protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/8'>"A" Conformation</scene>, the alcohol of the threonine side chain points towards the disulfide bond, engaging an ionic interaction between the two that prevents the Therodoxin Reductase from binding. Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/12'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space for the ligand to bind and reduction to occur. <br />
<br />
The active site of the protein is stabilized through a network of hydrogen bonds involving the two highly conserved residues, CVQC and WSGFRP. The crystal structure shows that interactions with one water molecule is necessary for the proper coordination between the conserved motifs to occur. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<br />
<br />
[[Image:Weblogocvqc.png|thumb|center|upright=2.5|Weblogo diagram showing highly conserved CVQC region of NrdH.]]<br />
<br />
Another highly conserved residue is the WSGFRP sequence. This nonpolar sequence is found on the surface of the molecule and is exposed to solvent. [[Image:Hydrophobic region pic.png|thumb| Hydrophobic region WSGFRP on the surface of MtNrdH (red) bound to ligand (green).]]<ref>DOI 10.1002/ijch.201300024</ref> <ref>PMID:21638687</ref> For this reason, it has been hypothesized that this sequence plays a role in the binding of thioredoxin reductase. <ref>Swastik, Phulera and Mande, Shekhar C. (2013) 4060.</ref> <br />
Arg-68 is responsible for the stabilization of the hydrophobic region of NrdH. Arg-68 has two distinct conformations. In the <scene name='69/694227/Arg_68_conformation_1/3'>first conformation</scene>, Arg-68 is hydrogen bonded to His- 60 and Asp-59. When Arg-68 shifts to its <scene name='69/694227/Arg_68_conformation_2/2'>second conformation</scene><br />
, it breaks it hydrogen bond with Asp-59. <ref>Swastik, Phulera and Mande, Shekhar C. (2013) 4057.</ref> This reduction in hydrogen bonding gives the hydrophobic region more flexibility and is thought to occur when NrdH is in its inactive state. <br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called ribonucleotide reductase (RNR) to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes.<ref>Swastik, Phulera and Mande, Shekhar C. (2013) 4056.</ref> Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thiordoxin, which are first reduced by glutadoxin reductase and thiordoxin reductase, respectively.<ref>Nelson, David L., and Michael M. Cox. Lehninger Principles of Biochemistry. 5th ed. New York: W.H. Freeman, 2008. 888-889.</ref> In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <ref>Swastik, Phulera and Mande, Shekhar C. (2013) 4056.</ref> <br />
<br />
<ref>Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref><br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|Ribonucleotide Reduction Class Ib general mechanism. The role of NrdH is highlighted.]] <br />
<br />
== Relevance ==<br />
<br />
Like most NrdHs, MtNrdH is similar in sequence to glutaredoxins, but structurally similar to thioredoxins. MtNrdH also accepts electrons from thiordoxin reductase, a characteristic of thiordoxins, but not glutaredoxins.<ref>Swastik, Phulera and Mande, Shekhar C. (2013) 4057.</ref> [[Image:Image-Super imposed molecules.png|thumb|left|Structural comparison of NrdHs with "thioredoxin folds": ''E. Coli'' NrdH (green), ''C. ammoniagenes'' NrdH (blue), ''M. tuberculosis'' NrdH (red)]]<ref>DOI 10.1002/ijch.201300024</ref> <ref>PMID:21638687</ref> <br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', and ''S. dysenteriae''. In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or theirodoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.Jmol reference <ref>DOI 10.1002/ijch.201300024</ref> article describing Jmol <ref>PMID:21638687</ref><br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2393808Sandbox Reserved 10612015-04-10T16:52:14Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='300' side='right' caption='Micobacterium tuberculosis NrdH' scene=''><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH is a small glutaredoxin-like protein involved in the electron transport chain in ribonucleotide reduction. <br />
<br />
== Background ==<br />
<br />
''Mycobacterium tuberculosis'' [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Wikipedia]resides in the lungs of a host and upon becoming active, results in symptoms such as chest pains, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013). The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. Tuberculosis is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative. <br />
<br />
<br />
== Structure == <br />
<br />
The structure of ''M. tuberculosis'' as determined by x-ray crystallography has 79 residues in a single polypeptide chain. <scene name='69/694228/Nrdh_structure/1'>NrdH Chrystal Structure</scene>. The active site (shown in green) is dominated by a disulphide bond between Cys-11 and Cys-14, which serves as the site of reduction by Theirodoxin reductase. <br />
<br />
Many theirodoxin-like proteins have a similar active site region, denoted as the theirodoxin fold, which occurs directly before the disulfide bond. The residues in this region, denoted by letters CVQC, are the most highly conserved of all areas of the protein across multiple species. Exactly how this structure relates to function is somewhat debated. A Threonine-7 reside directly across the theirodoxin fold from the disulphide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the Protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/8'>"A" Conformation</scene>, the alcohol of the threonine side chain points towards the disulfide bond, engaging an ionic interaction between the two that prevents the Therodoxin Reductase from binding. Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/12'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space for the ligand to bind and reduction to occur. <br />
<br />
The active site of the protein is stabilized through a network of hydrogen bonds involving the two highly conserved residues, CVQC and WSGFRP. The crystal structure shows that interactions with one water molecule is necessary for the proper coordination between the conserved motifs to occur. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<br />
<br />
[[Image:Weblogocvqc.png|thumb|center|upright=2.5|Weblogo diagram showing highly conserved CVQC region of NrdH.]]<br />
<br />
Another highly conserved residue is the WSGFRP sequence. This nonpolar sequence is found on the surface of the molecule and is exposed to solvent. [[Image:Hydrophobic region pic.png|thumb| Hydrophobic region WSGFRP on the surface of MtNrdH (red) bound to ligand (green).]]For this reason, it has been hypothesized that this sequence plays a role in the binding of thioredoxin reductase. <br />
Arg-68 is responsible for the stabilization of the hydrophobic region of NrdH. Arg-68 has two distinct conformations. In the <scene name='69/694227/Arg_68_conformation_1/3'>first conformation</scene>, Arg-68 is hydrogen bonded to His- 60 and Asp-59. When Arg-68 shifts to its <scene name='69/694227/Arg_68_conformation_2/2'>second conformation</scene><br />
, it breaks it hydrogen bond with Asp-59. This reduction in hydrogen bonding gives the hydrophobic region more flexibility and is thought to occur when NrdH is in its inactive state. <br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called ribonucleotide reductase (RNR) to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes. Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thiordoxin, which are first reduced by glutadoxin reductase and thiordoxin reductase, respectively. In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <br />
<br />
<ref>Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref><br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|Ribonucleotide Reduction Class Ib general mechanism. The role of NrdH is highlighted.]] <br />
<br />
== Relevance ==<br />
<br />
Like most NrdHs, MtNrdH is similar in sequence to glutaredoxins, but structurally similar to thioredoxins. MtNrdH also accepts electrons from thiordoxin reductase, a characteristic of thiordoxins, but not glutaredoxins. [[Image:Image-Super imposed molecules.png|thumb|left|Structural comparison of NrdHs with "thioredoxin folds": ''E. Coli'' NrdH (green), ''C. ammoniagenes'' NrdH (blue), ''M. tuberculosis'' NrdH (red)]]<br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', and ''S. dysenteriae''. In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or theirodoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.Jmol reference <ref>DOI 10.1002/ijch.201300024</ref> article describing Jmol <ref>PMID:21638687</ref><br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=File:Image-Super_imposed_molecules.png&diff=2393804File:Image-Super imposed molecules.png2015-04-10T16:47:31Z<p>Katelyn Burke: </p>
<hr />
<div></div>Katelyn Burkehttps://proteopedia.org/index.php?title=File:Super_imposed_molecules.png&diff=2393801File:Super imposed molecules.png2015-04-10T16:44:51Z<p>Katelyn Burke: uploaded a new version of "Image:Super imposed molecules.png": Three separate NrdHs with "thioredoxin" folds super imposed on one another: E. Coli NrdH (green), C. ammoniagenes NrdH (blue), and M. tuberculosis NrdH (red)</p>
<hr />
<div>Superimposed molecules picture</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2393796Sandbox Reserved 10612015-04-10T16:35:35Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='300' side='right' caption='Micobacterium tuberculosis NrdH' scene=''><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH is a small glutaredoxin-like protein involved in the electron transport chain in ribonucleotide reduction. <br />
<br />
== Background ==<br />
<br />
''Mycobacterium tuberculosis'' [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Wikipedia]resides in the lungs of a host and upon becoming active, results in symptoms such as chest pains, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013). The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. Tuberculosis is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative. <br />
<br />
<br />
== Structure == <br />
<br />
The structure of ''M. tuberculosis'' as determined by x-ray crystallography has 79 residues in a single polypeptide chain. <scene name='69/694228/Nrdh_structure/1'>NrdH Chrystal Structure</scene>. The active site (shown in green) is dominated by a disulphide bond between Cys-11 and Cys-14, which serves as the site of reduction by Theirodoxin reductase. <br />
<br />
Many theirodoxin-like proteins have a similar active site region, denoted as the theirodoxin fold, which occurs directly before the disulfide bond. The residues in this region, denoted by letters CVQC, are the most highly conserved of all areas of the protein across multiple species. Exactly how this structure relates to function is somewhat debated. A Threonine-7 reside directly across the theirodoxin fold from the disulphide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the Protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/8'>"A" Conformation</scene>, the alcohol of the threonine side chain points towards the disulfide bond, engaging an ionic interaction between the two that prevents the Therodoxin Reductase from binding. Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/12'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space for the ligand to bind and reduction to occur. <br />
<br />
The active site of the protein is stabilized through a network of hydrogen bonds involving the two highly conserved residues, CVQC and WSGFRP. The crystal structure shows that interactions with one water molecule is necessary for the proper coordination between the conserved motifs to occur. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<br />
<br />
[[Image:Weblogocvqc.png|thumb|center|upright=2.5|Weblogo diagram showing highly conserved CVQC region of NrdH.]]<br />
<br />
Another highly conserved residue is the WSGFRP sequence. This nonpolar sequence is found on the surface of the molecule and is exposed to solvent. [[Image:Hydrophobic region pic.png|thumb| Hydrophobic region WSGFRP on the surface of MtNrdH (red) bound to ligand (green).]]For this reason, it has been hypothesized that this sequence plays a role in the binding of thioredoxin reductase. <br />
Arg-68 is responsible for the stabilization of the hydrophobic region of NrdH. Arg-68 has two distinct conformations. In the <scene name='69/694227/Arg_68_conformation_1/3'>first conformation</scene>, Arg-68 is hydrogen bonded to His- 60 and Asp-59. When Arg-68 shifts to its <scene name='69/694227/Arg_68_conformation_2/2'>second conformation</scene><br />
, it breaks it hydrogen bond with Asp-59. This reduction in hydrogen bonding gives the hydrophobic region more flexibility and is thought to occur when NrdH is in its inactive state. <br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called ribonucleotide reductase (RNR) to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes. Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thiordoxin, which are first reduced by glutadoxin reductase and thiordoxin reductase, respectively. In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <br />
<br />
<ref>Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref><br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|Ribonucleotide Reduction Class Ib general mechanism. The role of NrdH is highlighted.]] <br />
<br />
== Relevance ==<br />
<br />
Like most NrdHs, MtNrdH is similar in sequence to glutaredoxins, but structurally similar to thioredoxins. MtNrdH also accepts electrons from thiordoxin reductase, a characteristic of thiordoxins, but not glutaredoxins. <br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', and ''S. dysenteriae''. In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or theirodoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.Jmol reference <ref>DOI 10.1002/ijch.201300024</ref> article describing Jmol <ref>PMID:21638687</ref><br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2393703Sandbox Reserved 10612015-04-10T01:06:32Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='300' side='right' caption='Micobacterium tuberculosis NrdH' scene=''><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH is a small glutaredoxin-like protein involved in the electron transport chain in ribonucleotide reduction. <br />
<br />
== Background ==<br />
<br />
''Mycobacterium tuberculosis'' [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Wikipedia]resides in the lungs of a host and upon becoming active, results in symptoms such as chest pains, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013). The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. Tuberculosis is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative. <br />
<br />
<br />
== Structure == <br />
<br />
The structure of ''M. tuberculosis'' as determined by x-ray crystallography has 79 residues in a single polypeptide chain. <scene name='69/694228/Nrdh_structure/1'>NrdH Chrystal Structure</scene>. The active site (shown in green) is dominated by a disulphide bond between Cys-11 and Cys-14, which serves as the site of reduction by Theirodoxin reductase. <br />
<br />
Many theirodoxin-like proteins have a similar active site region, denoted as the theirodoxin fold, which occurs directly before the disulfide bond. The residues in this region, denoted by letters CVQC, are the most highly conserved of all areas of the protein across multiple species. Exactly how this structure relates to function is somewhat debated. A Threonine-7 reside directly across the theirodoxin fold from the disulphide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the Protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/8'>"A" Conformation</scene>, the alcohol of the threonine side chain points towards the disulfide bond, engaging an ionic interaction between the two that prevents the Therodoxin Reductase from binding. Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/12'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space for the ligand to bind and reduction to occur. <br />
<br />
The active site of the protein is stabilized through a network of hydrogen bonds involving the two highly conserved residues, CVQC and WSGFRP. The crystal structure shows that interactions with one water molecule is necessary for the proper coordination between the conserved motifs to occur. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<br />
<br />
[[Image:Weblogocvqc.png|thumb|center|upright=2.5|Weblogo diagram showing highly conserved CVQC region of NrdH.]]<br />
<br />
Another highly conserved residue is the WSGFRP sequence. This nonpolar sequence is found on the surface of the molecule and is exposed to solvent. [[Image:Hydrophobic region pic.png|thumb| Hydrophobic region WSGFRP on the surface of MtNrdH (red) bound to ligand (green).]]For this reason, it has been hypothesized that this sequence plays a role in the binding of thioredoxin reductase. <br />
Arg-68 is responsible for the stabilization of the hydrophobic region of NrdH. Arg-68 has two distinct conformations. In the <scene name='69/694227/Arg_68_conformation_1/3'>first conformation</scene>, Arg-68 is hydrogen bonded to His- 60 and Asp-59. When Arg-68 shifts to its <scene name='69/694227/Arg_68_conformation_2/2'>second conformation</scene><br />
, it breaks it hydrogen bond with Asp-59. This reduction in hydrogen bonding gives the hydrophobic region more flexibility and is thought to occur when NrdH is in its inactive state. <br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called ribonucleotide reductase (RNR) to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes. Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thiordoxin, which are first reduced by glutadoxin reductase and thiordoxin reductase, respectively. In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <br />
<br />
<ref>Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref><br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|Ribonucleotide Reduction Class Ib general mechanism. The role of NrdH is highlighted.]] <br />
<br />
== Relevance ==<br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', and ''S. dysenteriae''. In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or theirodoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.Jmol reference <ref>DOI 10.1002/ijch.201300024</ref> article describing Jmol <ref>PMID:21638687</ref><br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2393701Sandbox Reserved 10612015-04-10T00:59:03Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='300' side='right' caption='Micobacterium tuberculosis NrdH' scene=''><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH is a small glutaredoxin-like protein involved in the electron transport chain in ribonucleotide reduction. <br />
<br />
== Background ==<br />
<br />
''Mycobacterium tuberculosis'' [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Wikipedia]resides in the lungs of a host and upon becoming active, results in symptoms such as chest pains, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013). The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. Tuberculosis is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative. <br />
<br />
<br />
== Structure == <br />
<br />
The structure of ''M. tuberculosis'' as determined by x-ray crystallography has 79 residues in a single polypeptide chain. <scene name='69/694228/Nrdh_structure/1'>NrdH Chrystal Structure</scene>. The active site (shown in green) is dominated by a disulphide bond between Cys-11 and Cys-14, which serves as the site of reduction by Theirodoxin reductase. <br />
<br />
Many theirodoxin-like proteins have a similar active site region, denoted as the theirodoxin fold, which occurs directly before the disulfide bond. The residues in this region, denoted by letters CVQC, are the most highly conserved of all areas of the protein across multiple species. Exactly how this structure relates to function is somewhat debated. A Threonine-7 reside directly across the theirodoxin fold from the disulphide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the Protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/8'>"A" Conformation</scene>, the alcohol of the threonine side chain points towards the disulfide bond, engaging an ionic interaction between the two that prevents the Therodoxin Reductase from binding. Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/12'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space for the ligand to bind and reduction to occur. <br />
<br />
The active site of the protein is stabilized through a network of hydrogen bonds involving the two highly conserved residues, CVQC and WSGFRP. The crystal structure shows that interactions with one water molecule is necessary for the proper coordination between the conserved motifs to occur. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<br />
<br />
[[Image:Weblogocvqc.png|thumb|center|upright=2.5|Weblogo diagram showing highly conserved CVQC region of NrdH.]]<br />
<br />
Another highly conserved residue is the WSGFRP sequence. This nonpolar sequence is found on the surface of the molecule and is exposed to solvent. [[Image:Hydrophobic region pic.png|thumb| Hydrophobic region WSGFRP on the surface of MtNrdH (red) bound to ligand (green).]]For this reason, it has been hypothesized that this sequence plays a role in the binding of thioredoxin reductase. <br />
Arg-68 is responsible for the stabilization of the hydrophobic region of NrdH. Arg-68 has two distinct conformations. In the <scene name='69/694227/Arg_68_conformation_1/3'>first conformation</scene>, Arg-68 is hydrogen bonded to His- 60 and Asp-59. When Arg-68 shifts to its second conformation, it breaks it hydrogen bond with Asp-59. This reduction in hydrogen bonding gives the hydrophobic region more flexibility and is thought to occur when NrdH is in its inactive state. <br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called ribonucleotide reductase (RNR) to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes. Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thiordoxin, which are first reduced by glutadoxin reductase and thiordoxin reductase, respectively. In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <br />
<br />
<ref>Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref><br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|Ribonucleotide Reduction Class Ib general mechanism. The role of NrdH is highlighted.]] <br />
<br />
== Relevance ==<br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', and ''S. dysenteriae''. In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or theirodoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.Jmol reference <ref>DOI 10.1002/ijch.201300024</ref> article describing Jmol <ref>PMID:21638687</ref><br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2393700Sandbox Reserved 10612015-04-10T00:57:59Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='300' side='right' caption='Micobacterium tuberculosis NrdH' scene=''><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH is a small glutaredoxin-like protein involved in the electron transport chain in ribonucleotide reduction. <br />
<br />
== Background ==<br />
<br />
''Mycobacterium tuberculosis'' [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Wikipedia]resides in the lungs of a host and upon becoming active, results in symptoms such as chest pains, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013). The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. Tuberculosis is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative. <br />
<br />
<br />
== Structure == <br />
<br />
The structure of ''M. tuberculosis'' as determined by x-ray crystallography has 79 residues in a single polypeptide chain. <scene name='69/694228/Nrdh_structure/1'>NrdH Chrystal Structure</scene>. The active site (shown in green) is dominated by a disulphide bond between Cys-11 and Cys-14, which serves as the site of reduction by Theirodoxin reductase. <br />
<br />
Many theirodoxin-like proteins have a similar active site region, denoted as the theirodoxin fold, which occurs directly before the disulfide bond. The residues in this region, denoted by letters CVQC, are the most highly conserved of all areas of the protein across multiple species. Exactly how this structure relates to function is somewhat debated. A Threonine-7 reside directly across the theirodoxin fold from the disulphide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the Protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/8'>"A" Conformation</scene>, the alcohol of the threonine side chain points towards the disulfide bond, engaging an ionic interaction between the two that prevents the Therodoxin Reductase from binding. [[Image:Disulfide bond with ligand.png|thumb|ionic interaction between Thr-7 residue and disulfide bond which occurs across the theirodoxin fold]] Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/12'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space for the ligand to bind and reduction to occur. <br />
<br />
The active site of the protein is stabilized through a network of hydrogen bonds involving the two highly conserved residues, CVQC and WSGFRP. The crystal structure shows that interactions with one water molecule is necessary for the proper coordination between the conserved motifs to occur. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<br />
<br />
[[Image:Weblogocvqc.png|thumb|center|upright=2.5|Weblogo diagram showing highly conserved CVQC region of NrdH.]]<br />
<br />
Another highly conserved residue is the WSGFRP sequence. This nonpolar sequence is found on the surface of the molecule and is exposed to solvent. [[Image:Hydrophobic region pic.png|thumb| Hydrophobic region WSGFRP on the surface of MtNrdH (red) bound to ligand (green).]]For this reason, it has been hypothesized that this sequence plays a role in the binding of thioredoxin reductase. <br />
Arg-68 is responsible for the stabilization of the hydrophobic region of NrdH. Arg-68 has two distinct conformations. In the <scene name='69/694227/Arg_68_conformation_1/3'>first conformation</scene>, Arg-68 is hydrogen bonded to His- 60 and Asp-59. When Arg-68 shifts to its second conformation, it breaks it hydrogen bond with Asp-59. This reduction in hydrogen bonding gives the hydrophobic region more flexibility and is thought to occur when NrdH is in its inactive state. <br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called ribonucleotide reductase (RNR) to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes. Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thiordoxin, which are first reduced by glutadoxin reductase and thiordoxin reductase, respectively. In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <br />
<br />
<ref>Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref><br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|Ribonucleotide Reduction Class Ib general mechanism. The role of NrdH is highlighted.]] <br />
<br />
== Relevance ==<br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', and ''S. dysenteriae''. In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or theirodoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.Jmol reference <ref>DOI 10.1002/ijch.201300024</ref> article describing Jmol <ref>PMID:21638687</ref><br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1060&diff=2393698Sandbox Reserved 10602015-04-10T00:55:58Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==Your Heading Here (maybe something like 'Structure')==<br />
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
<scene name='69/694227/Arg_68_conformation_1/3'>TextToBeDisplayed</scene><br />
<br />
<scene name='69/694227/Arg_68_conformation_1/2'>lets try again</scene><br />
<br />
<scene name='69/694227/Arg_68_conformation_2/1'>Conformation 2</scene><br />
<br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1060&diff=2393696Sandbox Reserved 10602015-04-10T00:49:51Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==Your Heading Here (maybe something like 'Structure')==<br />
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
<br />
<scene name='69/694227/Arg_68_conformation_1/1'>Conformation 1</scene><br />
<br />
<scene name='69/694227/Arg_68_conformation_1/2'>lets try again</scene><br />
<br />
<scene name='69/694227/Arg_68_conformation_2/1'>Conformation 2</scene><br />
<br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2393692Sandbox Reserved 10612015-04-10T00:38:55Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='300' side='right' caption='Micobacterium tuberculosis NrdH' scene=''><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH is a small glutaredoxin-like protein involved in the electron transport chain in ribonucleotide reduction. <br />
<br />
== Background ==<br />
<br />
''Mycobacterium tuberculosis'' [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Wikipedia]resides in the lungs of a host and upon becoming active, results in symptoms such as chest pains, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013). The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. Tuberculosis is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative. <br />
<br />
<br />
== Structure == <br />
<br />
The structure of ''M. tuberculosis'' as determined by x-ray crystallography has 79 residues in a single polypeptide chain. <scene name='69/694228/Nrdh_structure/1'>NrdH Chrystal Structure</scene>. The active site (shown in green) is dominated by a disulphide bond between Cys-11 and Cys-14, which serves as the site of reduction by Theirodoxin reductase. <br />
<br />
Many theirodoxin-like proteins have a similar active site region, denoted as the theirodoxin fold, which occurs directly before the disulfide bond. The residues in this region, denoted by letters CVQC, are the most highly conserved of all areas of the protein across multiple species. Exactly how this structure relates to function is somewhat debated. A Threonine-7 reside directly across the theirodoxin fold from the disulphide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the Protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/8'>"A" Conformation</scene>, the alcohol of the threonine side chain points towards the disulfide bond, engaging an ionic interaction between the two that prevents the Therodoxin Reductase from binding. [[Image:Disulfide bond with ligand.png|thumb|ionic interaction between Thr-7 residue and disulfide bond which occurs across the theirodoxin fold]] Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/12'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space for the ligand to bind and reduction to occur. <br />
<br />
The active site of the protein is stabilized through a network of hydrogen bonds involving the two highly conserved residues, CVQC and WSGFRP. The crystal structure shows that interactions with one water molecule is necessary for the proper coordination between the conserved motifs to occur. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<br />
<br />
[[Image:Weblogocvqc.png|thumb|center|upright=2.5|Weblogo diagram showing highly conserved CVQC region of NrdH.]]<br />
<br />
Another highly conserved residue is the WSGFRP sequence. This nonpolar sequence is found on the surface of the molecule and is exposed to solvent. [[Image:Hydrophobic region pic.png|thumb| Hydrophobic region WSGFRP on the surface of MtNrdH (red) bound to ligand (green).]]For this reason, it has been hypothesized that this sequence plays a role in the binding of thioredoxin reductase. <br />
<scene name='69/694227/Arg_68_conformation_2/1'>Arg-68</scene> is responsible for the stabilization of the hydrophobic region of NrdH. Arg-68 has two distinct conformations. In the first conformation, Arg-68 is hydrogen bonded to His- 60 and Asp-59. When Arg-68 shifts to its second conformation, it breaks it hydrogen bond with Asp-59. This reduction in hydrogen bonding gives the hydrophobic region more flexibility and is thought to occur when NrdH is in its inactive state. <br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called ribonucleotide reductase (RNR) to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes. Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thiordoxin, which are first reduced by glutadoxin reductase and thiordoxin reductase, respectively. In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <br />
<br />
<ref>Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref><br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|Ribonucleotide Reduction Class Ib general mechanism. The role of NrdH is highlighted.]] <br />
<br />
== Relevance ==<br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', and ''S. dysenteriae''. In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or theirodoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.Jmol reference <ref>DOI 10.1002/ijch.201300024</ref> article describing Jmol <ref>PMID:21638687</ref><br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2393690Sandbox Reserved 10612015-04-10T00:34:07Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='300' side='right' caption='Micobacterium tuberculosis NrdH' scene=''><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH is a small glutaredoxin-like protein involved in the electron transport chain in ribonucleotide reduction. <br />
<br />
== Background ==<br />
<br />
''Mycobacterium tuberculosis'' [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Wikipedia]resides in the lungs of a host and upon becoming active, results in symptoms such as chest pains, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013). The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. Tuberculosis is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative. <br />
<br />
<br />
== Structure == <br />
<br />
The structure of ''M. tuberculosis'' as determined by x-ray crystallography has 79 residues in a single polypeptide chain. <scene name='69/694228/Nrdh_structure/1'>NrdH Chrystal Structure</scene>. The active site (shown in green) is dominated by a disulphide bond between Cys-11 and Cys-14, which serves as the site of reduction by Theirodoxin reductase. <br />
<br />
Many theirodoxin-like proteins have a similar active site region, denoted as the theirodoxin fold, which occurs directly before the disulfide bond. The residues in this region, denoted by letters CVQC, are the most highly conserved of all areas of the protein across multiple species. Exactly how this structure relates to function is somewhat debated. A Threonine-7 reside directly across the theirodoxin fold from the disulphide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the Protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/8'>"A" Conformation</scene>, the alcohol of the threonine side chain points towards the disulfide bond, engaging an ionic interaction between the two that prevents the Therodoxin Reductase from binding. [[Image:Disulfide bond with ligand.png|thumb|ionic interaction between Thr-7 residue and disulfide bond which occurs across the theirodoxin fold]] Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/12'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space for the ligand to bind and reduction to occur. <br />
<br />
The active site of the protein is stabilized through a network of hydrogen bonds involving the two highly conserved residues, CVQC and WSGFRP. The crystal structure shows that interactions with one water molecule is necessary for the proper coordination between the conserved motifs to occur. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<br />
<br />
[[Image:Weblogocvqc.png|thumb|center|upright=2.5|Weblogo diagram showing highly conserved CVQC region of NrdH.]]<br />
<br />
Another highly conserved residue is the WSGFRP sequence. This nonpolar sequence is found on the surface of the molecule and is exposed to solvent. [[Image:Image:Hydrophobic region pic.png|thumb]]For this reason, it has been hypothesized that this sequence plays a role in the binding of thioredoxin reductase. <br />
Arg-68 is responsible for the stabilization of the hydrophobic region of NrdH. Arg-68 has two distinct conformations. In the first conformation, Arg-68 is hydrogen bonded to His- 60 and Asp-59. When Arg-68 shifts to its second conformation, it breaks it hydrogen bond with Asp-59. This reduction in hydrogen bonding gives the hydrophobic region more flexibility and is thought to occur when NrdH is in its inactive state. <br />
<br />
<br />
<scene name='69/694227/Arg_68_conformation_2/1'>TextToBeDisplayed</scene><br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called ribonucleotide reductase (RNR) to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes. Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thiordoxin, which are first reduced by glutadoxin reductase and thiordoxin reductase, respectively. In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <br />
<br />
<ref>Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref><br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|Ribonucleotide Reduction Class Ib general mechanism. The role of NrdH is highlighted.]] <br />
<br />
== Relevance ==<br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', and ''S. dysenteriae''. In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or theirodoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.Jmol reference <ref>DOI 10.1002/ijch.201300024</ref> article describing Jmol <ref>PMID:21638687</ref><br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2393687Sandbox Reserved 10612015-04-10T00:29:59Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='300' side='right' caption='Micobacterium tuberculosis NrdH' scene=''><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH is a small glutaredoxin-like protein involved in the electron transport chain in ribonucleotide reduction. <br />
<br />
== Background ==<br />
<br />
''Mycobacterium tuberculosis'' [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Wikipedia]resides in the lungs of a host and upon becoming active, results in symptoms such as chest pains, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013). The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. Tuberculosis is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative. <br />
<br />
<br />
== Structure == <br />
<br />
The structure of ''M. tuberculosis'' as determined by x-ray crystallography has 79 residues in a single polypeptide chain. <scene name='69/694228/Nrdh_structure/1'>NrdH Chrystal Structure</scene>. The active site (shown in green) is dominated by a disulphide bond between Cys-11 and Cys-14, which serves as the site of reduction by Theirodoxin reductase. <br />
<br />
Many theirodoxin-like proteins have a similar active site region, denoted as the theirodoxin fold, which occurs directly before the disulfide bond. The residues in this region, denoted by letters CVQC, are the most highly conserved of all areas of the protein across multiple species. Exactly how this structure relates to function is somewhat debated. A Threonine-7 reside directly across the theirodoxin fold from the disulphide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the Protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/8'>"A" Conformation</scene>, the alcohol of the threonine side chain points towards the disulfide bond, engaging an ionic interaction between the two that prevents the Therodoxin Reductase from binding. [[Image:Disulfide bond with ligand.png|thumb|ionic interaction between Thr-7 residue and disulfide bond which occurs across the theirodoxin fold]] Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/12'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space for the ligand to bind and reduction to occur. <br />
<br />
The active site of the protein is stabilized through a network of hydrogen bonds involving the two highly conserved residues, CVQC and WSGFRP. The crystal structure shows that interactions with one water molecule is necessary for the proper coordination between the conserved motifs to occur. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<br />
<br />
[[Image:Weblogocvqc.png|thumb|center|upright=2.5|Weblogo diagram showing highly conserved CVQC region of NrdH.]]<br />
<br />
Another highly conserved residue is the WSGFRP sequence. This nonpolar sequence is found on the surface of the molecule and is exposed to solvent. For this reason, it has been hypothesized that this sequence plays a role in the binding of thioredoxin reductase. <br />
Arg-68 is responsible for the stabilization of the hydrophobic region of NrdH. Arg-68 has two distinct conformations. In the first conformation, Arg-68 is hydrogen bonded to His- 60 and Asp-59. When Arg-68 shifts to its second conformation, it breaks it hydrogen bond with Asp-59. This reduction in hydrogen bonding gives the hydrophobic region more flexibility and is thought to occur when NrdH is in its inactive state. <br />
<br />
<br />
<scene name='69/694227/Arg_68_conformation_2/1'>TextToBeDisplayed</scene><br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called ribonucleotide reductase (RNR) to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes. Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thiordoxin, which are first reduced by glutadoxin reductase and thiordoxin reductase, respectively. In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <br />
<br />
<ref>Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref><br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|Ribonucleotide Reduction Class Ib general mechanism. The role of NrdH is highlighted.]] <br />
<br />
== Relevance ==<br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', and ''S. dysenteriae''. In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or theirodoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.Jmol reference <ref>DOI 10.1002/ijch.201300024</ref> article describing Jmol <ref>PMID:21638687</ref><br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2393675Sandbox Reserved 10612015-04-10T00:16:15Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='300' side='right' caption='Micobacterium tuberculosis NrdH' scene=''><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH is a small glutaredoxin-like protein involved in the electron transport chain that eventually leads to ribonucleotide reduction. <br />
<br />
This page is for Bryant Dawson and Kate Burke hehehe<br />
<br />
<br />
== Background ==<br />
<br />
''Mycobacterium tuberculosis'' [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Wikipedia]resides in the lungs of a host and upon becoming active, results in symptoms such as chest pains, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013). The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. Tuberculosis is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative. <br />
<br />
<br />
== Structure == <br />
<br />
The structure of ''M. tuberculosis'' as determined by x-ray crystallography has 79 residues in a single polypeptide chain. <scene name='69/694228/Nrdh_structure/1'>NrdH Chrystal Structure</scene>. The active site (shown in green) is dominated by a disulphide bond between Cys-11 and Cys-14, which serves as the site of reduction by Theirodoxin reductase. <br />
<br />
Many theirodoxin-like proteins have a similar active site region, denoted as the theirodoxin fold, which occurs directly before the disulfide bond. The residues in this region, denoted by letters CVQC, are the most highly conserved of all areas of the protein across multiple species. Exactly how this structure relates to function is somewhat debated. A Threonine-7 reside directly across the theirodoxin fold from the disulphide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the Protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/8'>"A" Conformation</scene>, the alcohol of the threonine side chain points towards the disulfide bond, engaging an ionic interaction between the two that prevents the Therodoxin Reductase from binding. [[Image:Disulfide bond with ligand.png|thumb|ionic interaction between Thr-7 residue and disulfide bond which occurs across the theirodoxin fold]] Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/12'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space for the ligand to bind and reduction to occur. <br />
<br />
The active site of the protein is stabilized through a network of hydrogen bonds involving the two highly conserved residues, CVQC and WSGFRP. The crystal structure shows that interactions with one water molecule is necessary for the proper coordination between the conserved motifs to occur. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<br />
<br />
<scene name='69/694227/Arg_68_conformation_2/1'>TextToBeDisplayed</scene><br />
<br />
== Function ==<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called ribonucleotide reductase (RNR) to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes. Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thiordoxin, which are first reduced by glutadoxin reductase and thiordoxin reductase, respectively. In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <br />
<br />
<ref>Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref><br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|Ribonucleotide Reduction Class Ib general mechanism. The role of NrdH is highlighted.]] <br />
<br />
== Relevance ==<br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', and ''S. dysenteriae''. In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or theirodoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.Jmol reference <ref>DOI 10.1002/ijch.201300024</ref> article describing Jmol <ref>PMID:21638687</ref><br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2393671Sandbox Reserved 10612015-04-10T00:13:18Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='4hs1' size='300' side='right' caption='Micobacterium tuberculosis NrdH' scene=''><br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH is a small glutaredoxin-like protein involved in the electron transport chain that eventually leads to ribonucleotide reduction. <br />
<br />
This page is for Bryant Dawson and Kate Burke hehehe<br />
<br />
<br />
== Background ==<br />
<br />
''Mycobacterium tuberculosis'' [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Wikipedia]resides in the lungs of a host and upon becoming active, results in symptoms such as chest pains, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013). The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. Tuberculosis is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative. <br />
<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called ribonucleotide reductase (RNR) to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes. Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thiordoxin, which are first reduced by glutadoxin reductase and thiordoxin reductase, respectively. In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <br />
<br />
<ref>Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref><br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.5|Ribonucleotide Reduction Class Ib general mechanism. The role of NrdH is highlighted.]] <br />
<br />
<br />
== Structure == <br />
<br />
The structure of ''M. tuberculosis'' as determined by x-ray crystallography has 79 residues in a single polypeptide chain. <scene name='69/694228/Nrdh_structure/1'>NrdH Chrystal Structure</scene>. The active site (shown in green) is dominated by a disulphide bond between Cys-11 and Cys-14, which serves as the site of reduction by Theirodoxin reductase. <br />
<br />
Many theirodoxin-like proteins have a similar active site region, denoted as the theirodoxin fold, which occurs directly before the disulfide bond. The residues in this region, denoted by letters CVQC, are the most highly conserved of all areas of the protein across multiple species. Exactly how this structure relates to function is somewhat debated. A Threonine-7 reside directly across the theirodoxin fold from the disulphide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the Protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/8'>"A" Conformation</scene>, the alcohol of the threonine side chain points towards the disulfide bond, engaging an ionic interaction between the two that prevents the Therodoxin Reductase from binding. [[Image:Disulfide bond with ligand.png|thumb|ionic interaction between Thr-7 residue and disulfide bond which occurs across the theirodoxin fold]] Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/12'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space for the ligand to bind and reduction to occur. <br />
<br />
The active site of the protein is stabilized through a network of hydrogen bonds involving the two highly conserved residues, CVQC and WSGFRP. The crystal structure shows that interactions with one water molecule is necessary for the proper coordination between the conserved motifs to occur. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction.<br />
<br />
== Function ==<br />
<scene name='69/694227/Arg_68_conformation_2/1'>TextToBeDisplayed</scene><br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', and ''S. dysenteriae''. In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or theirodoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.Jmol reference <ref>DOI 10.1002/ijch.201300024</ref> article describing Jmol <ref>PMID:21638687</ref><br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2393662Sandbox Reserved 10612015-04-09T23:56:27Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
This page is for Bryant Dawson and Kate Burke hehehe<br />
<br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH is a small glutaredoxin-like protein involved in the electron transport chain that eventually leads to ribonucleotide reduction. <br />
<br />
== Background ==<br />
<br />
''Mycobacterium tuberculosis'' [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Wikipedia]resides in the lungs of a host and upon becoming active, results in symptoms such as chest pains, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013). The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. Tuberculosis is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative. <br />
<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called ribonucleotide reductase (RNR) to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes. Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP to dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thiordoxin, which are first reduced by glutadoxin reductase and thiordoxin reductase, respectively. In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <br />
<br />
<ref>Makhlynets, O., Boal, A. K., Rhodes, D. V., Kitten, T., Rosenzweig, A. C., & Stubbe, J. (2014). Streptococcus sanguinis Class Ib Ribonucleotide Reductase: HIGH ACTIVITY WITH BOTH IRON AND MANGANESE COFACTORS AND STRUCTURAL INSIGHTS. The Journal of Biological Chemistry, 289(9), 6259–6272. doi:10.1074/jbc.M113.533554.</ref><br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|center|upright=2.0|Ribonucleotide Reduction Class Ib general mechanism. The role of NrdH is highlighted.]] <br />
<br />
<br />
== Structure == <br />
<br />
The structure of ''M. tuberculosis'' as determined by x-ray crystallography has 79 residues in a single polypeptide chain. <scene name='69/694228/Nrdh_structure/1'>NrdH Chrystal Structure</scene>. The active site (shown in green) is dominated by a disulphide bond between Cys-11 and Cys-14, which serves as the site of reduction by Theirodoxin reductase. <br />
<br />
Many theirodoxin-like proteins have a similar active site region, denoted as the theirodoxin fold, which occurs directly before the disulfide bond. The residues in this region, denoted by letters CVQC, are the most highly conserved of all areas of the protein across multiple species. Exactly how this structure relates to function is somewhat debated. A Threonine-7 reside directly across the theirodoxin fold from the disulphide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the Protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/8'>"A" Conformation</scene>, the alcohol of the threonine side chain points towards the disulfide bond, engaging an ionic interaction between the two that prevents the Therodoxin Reductase from binding. [[Image:Disulfide bond with ligand.png|thumb|ionic interaction between Thr-7 residue and disulfide bond which occurs across the theirodoxin fold]] Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/12'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space for the ligand to bind and reduction to occur. <br />
<br />
The active site of the protein is stabilized through a network of hydrogen bonds involving the two highly conserved residues, CVQC and WSGFRP. The crystal structure shows that interactions with one water molecule is necessary for the proper coordination between the conserved motifs to occur. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction. [[Image:Hydrogen coordination without measurements.png|thumb|the H-bond interactions between conserved residues CVQC, WSGFRP, and a water molecule]]<br />
<br />
== Function ==<br />
<scene name='69/694227/Arg_68_conformation_2/1'>TextToBeDisplayed</scene><br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', and ''S. dysenteriae''. In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or theirodoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<br />
{{reflist}}</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2393639Sandbox Reserved 10612015-04-09T23:20:32Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
This page is for Bryant Dawson and Kate Burke hehehe<br />
<br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH is a small glutaredoxin-like protein involved in the electron transport chain that eventually leads to ribonucleotide reduction. <br />
<br />
== Background ==<br />
<br />
''Mycobacterium tuberculosis'' [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Wikipedia]resides in the lungs of a host and upon becoming active, results in symptoms such as chest pains, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013). The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. Tuberculosis is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative. <br />
<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called ribonucleotide reductase (RNR) to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes. Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thiordoxin, which are first reduced by glutadoxin reductase and thiordoxin reductase, respectively. In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <br />
<br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|]]<br />
<br />
<br />
== Structure == <br />
<br />
The structure of ''M. tuberculosis'' as determined by x-ray crystallography has 79 residues in a single polypeptide chain. <scene name='69/694228/Nrdh_structure/1'>NrdH Chrystal Structure</scene>. The active site (shown in green) is dominated by a disulphide bond between Cys-11 and Cys-14, which serves as the site of reduction by Theirodoxin reductase. <br />
<br />
Many theirodoxin-like proteins have a similar active site region, denoted as the theirodoxin fold, which occurs directly before the disulfide bond. The residues in this region, denoted by letters CVQC, are the most highly conserved of all areas of the protein across multiple species. Exactly how this structure relates to function is somewhat debated. A Threonine-7 reside directly across the theirodoxin fold from the disulphide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the Protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/8'>"A" Conformation</scene>, the alcohol of the threonine side chain points towards the disulfide bond, engaging an ionic interaction between the two that prevents the Therodoxin Reductase from binding. [[Image:Disulfide bond with ligand.png|thumb|ionic interaction between Thr-7 residue and disulfide bond which occurs across the theirodoxin fold]] Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/12'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space for the ligand to bind and reduction to occur. <br />
<br />
The active site of the protein is stabilized through a network of hydrogen bonds involving the two highly conserved residues, CVQC and WSGFRP. The crystal structure shows that interactions with one water molecule is necessary for the proper coordination between the conserved motifs to occur. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction. [[Image:Hydrogen coordination without measurements.png|thumb|the H-bond interactions between conserved residues CVQC, WSGFRP, and a water molecule]]<br />
<br />
== Function ==<br />
<scene name='69/694227/Arg_68_conformation_2/1'>TextToBeDisplayed</scene><br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', and ''S. dysenteriae''. In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or theirodoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2393638Sandbox Reserved 10612015-04-09T23:19:44Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
This page is for Bryant Dawson and Kate Burke hehehe<br />
<br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH is a small glutaredoxin-like protein involved in the electron transport chain that eventually leads to ribonucleotide reduction. <br />
<br />
== Background ==<br />
<br />
''Mycobacterium tuberculosis'' [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Wikipedia]resides in the lungs of a host and upon becoming active, results in symptoms such as chest pains, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013). The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. Tuberculosis is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative. <br />
<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called ribonucleotide reductase (RNR) to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes. Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thiordoxin, which are first reduced by glutadoxin reductase and thiordoxin reductase, respectively. In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <br />
<br />
[[Image:Ribonucleotide Reduction Class 1b.jpg|thumb|]]<br />
<br />
== Structure == <br />
<br />
The structure of ''M. tuberculosis'' as determined by x-ray crystallography has 79 residues in a single polypeptide chain. <scene name='69/694228/Nrdh_structure/1'>NrdH Chrystal Structure</scene>. The active site (shown in green) is dominated by a disulphide bond between Cys-11 and Cys-14, which serves as the site of reduction by Theirodoxin reductase. <br />
<br />
Many theirodoxin-like proteins have a similar active site region, denoted as the theirodoxin fold, which occurs directly before the disulfide bond. The residues in this region, denoted by letters CVQC, are the most highly conserved of all areas of the protein across multiple species. Exactly how this structure relates to function is somewhat debated. A Threonine-7 reside directly across the theirodoxin fold from the disulphide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the Protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/8'>"A" Conformation</scene>, the alcohol of the threonine side chain points towards the disulfide bond, engaging an ionic interaction between the two that prevents the Therodoxin Reductase from binding. [[Image:Disulfide bond with ligand.png|thumb|ionic interaction between Thr-7 residue and disulfide bond which occurs across the theirodoxin fold]] Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/12'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space for the ligand to bind and reduction to occur. <br />
<br />
The active site of the protein is stabilized through a network of hydrogen bonds involving the two highly conserved residues, CVQC and WSGFRP. The crystal structure shows that interactions with one water molecule is necessary for the proper coordination between the conserved motifs to occur. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction. [[Image:Hydrogen coordination without measurements.png|thumb|the H-bond interactions between conserved residues CVQC, WSGFRP, and a water molecule]]<br />
<br />
== Function ==<br />
<scene name='69/694227/Arg_68_conformation_2/1'>TextToBeDisplayed</scene><br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', and ''S. dysenteriae''. In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or theirodoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2393637Sandbox Reserved 10612015-04-09T23:17:26Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
This page is for Bryant Dawson and Kate Burke hehehe<br />
<br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH is a small glutaredoxin-like protein involved in the electron transport chain that eventually leads to ribonucleotide reduction. <br />
<br />
== Background ==<br />
<br />
''Mycobacterium tuberculosis'' [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Wikipedia]resides in the lungs of a host and upon becoming active, results in symptoms such as chest pains, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013). The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. Tuberculosis is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative. <br />
<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called ribonucleotide reductase (RNR) to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes. Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thiordoxin, which are first reduced by glutadoxin reductase and thiordoxin reductase, respectively. In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <br />
<br />
[[Image:Disulfide bond with ligand.png|thumb|ionic interaction between Thr-7 residue and disulfide bond which occurs across the theirodoxin fold]]<br />
<br />
== Structure == <br />
<br />
The structure of ''M. tuberculosis'' as determined by x-ray crystallography has 79 residues in a single polypeptide chain. <scene name='69/694228/Nrdh_structure/1'>NrdH Chrystal Structure</scene>. The active site (shown in green) is dominated by a disulphide bond between Cys-11 and Cys-14, which serves as the site of reduction by Theirodoxin reductase. <br />
<br />
Many theirodoxin-like proteins have a similar active site region, denoted as the theirodoxin fold, which occurs directly before the disulfide bond. The residues in this region, denoted by letters CVQC, are the most highly conserved of all areas of the protein across multiple species. Exactly how this structure relates to function is somewhat debated. A Threonine-7 reside directly across the theirodoxin fold from the disulphide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the Protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/8'>"A" Conformation</scene>, the alcohol of the threonine side chain points towards the disulfide bond, engaging an ionic interaction between the two that prevents the Therodoxin Reductase from binding. [[Image:Disulfide bond with ligand.png|thumb|ionic interaction between Thr-7 residue and disulfide bond which occurs across the theirodoxin fold]] Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/12'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space for the ligand to bind and reduction to occur. <br />
<br />
The active site of the protein is stabilized through a network of hydrogen bonds involving the two highly conserved residues, CVQC and WSGFRP. The crystal structure shows that interactions with one water molecule is necessary for the proper coordination between the conserved motifs to occur. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction. [[Image:Hydrogen coordination without measurements.png|thumb|the H-bond interactions between conserved residues CVQC, WSGFRP, and a water molecule]]<br />
<br />
== Function ==<br />
<scene name='69/694227/Arg_68_conformation_2/1'>TextToBeDisplayed</scene><br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', and ''S. dysenteriae''. In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or theirodoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Katelyn Burkehttps://proteopedia.org/index.php?title=File:Ribonucleotide_Reduction_Class_1b.jpg&diff=2393635File:Ribonucleotide Reduction Class 1b.jpg2015-04-09T23:14:30Z<p>Katelyn Burke: Ribonucleotide Reduction Class 1b</p>
<hr />
<div>Ribonucleotide Reduction Class 1b</div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2393634Sandbox Reserved 10612015-04-09T23:10:20Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
This page is for Bryant Dawson and Kate Burke hehehe<br />
<br />
== Overview ==<br />
''Mycobacterium tuberculosis'' NrdH is a small glutaredoxin-like protein involved in the electron transport chain that eventually leads to ribonucleotide reduction. <br />
<br />
== Background ==<br />
<br />
''Mycobacterium tuberculosis'' [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Wikipedia]resides in the lungs of a host and upon becoming active, results in symptoms such as chest pains, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013). The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. Tuberculosis is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative. <br />
<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called ribonucleotide reductase (RNR) to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes. Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
<br />
Class I RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thiordoxin, which are first reduced by glutadoxin reductase and thiordoxin reductase, respectively. In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <br />
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<br />
== Structure == <br />
<br />
The structure of ''M. tuberculosis'' as determined by x-ray crystallography has 79 residues in a single polypeptide chain. <scene name='69/694228/Nrdh_structure/1'>NrdH Chrystal Structure</scene>. The active site (shown in green) is dominated by a disulphide bond between Cys-11 and Cys-14, which serves as the site of reduction by Theirodoxin reductase. <br />
<br />
Many theirodoxin-like proteins have a similar active site region, denoted as the theirodoxin fold, which occurs directly before the disulfide bond. The residues in this region, denoted by letters CVQC, are the most highly conserved of all areas of the protein across multiple species. Exactly how this structure relates to function is somewhat debated. A Threonine-7 reside directly across the theirodoxin fold from the disulphide bond has been suggested to adopt two different conformations which differentially affect the redox abilities of the Protein. In the <scene name='69/694228/Nrdh_ligand_binding_site/8'>"A" Conformation</scene>, the alcohol of the threonine side chain points towards the disulfide bond, engaging an ionic interaction between the two that prevents the Therodoxin Reductase from binding. [[Image:Disulfide bond with ligand.png|thumb|ionic interaction between Thr-7 residue and disulfide bond which occurs across the theirodoxin fold]] Alternatively, in the <scene name='69/694228/Nrdh_ligand_binding_site/12'>"B" Conformation</scene>, the alcohol points in the opposite direction, allowing sufficient space for the ligand to bind and reduction to occur. <br />
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The active site of the protein is stabilized through a network of hydrogen bonds involving the two highly conserved residues, CVQC and WSGFRP. The crystal structure shows that interactions with one water molecule is necessary for the proper coordination between the conserved motifs to occur. These hydrogen bonds orient the important residues in the most optimal position to promote oxidation and reduction. [[Image:Hydrogen coordination without measurements.png|thumb|the H-bond interactions between conserved residues CVQC, WSGFRP, and a water molecule]]<br />
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== Function ==<br />
<scene name='69/694227/Arg_68_conformation_2/1'>TextToBeDisplayed</scene><br />
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== Disease ==<br />
<br />
== Relevance ==<br />
<br />
Similar structures of NrdH have been isolated in other primitive species including ''E. coli'', ''S. pyogenes'', ''S. typhimurium'', ''D. deserti'', ''S. flexneri 2457T'', and ''S. dysenteriae''. In higher order multi-cellular organisms, however the NrdH protein is replaced by more complex glutaredoxins or theirodoxins. This observation leads some to speculate that NrdH is one of the very first ancestors in the ribonucleotide reduction pathway. If this is true, NrdH can be seen as a critical protein that allowed for the development of DNA-based life since deoxyribonucleotides could not have existed without the ribonucleotide reduction pathway. A better understanding of the evolutionary timeline of NrdH and similar proteins could shed greater light onto the RNA Wold Hypothesis, specifically describing the time frame of emergence of DNA based life. <br />
<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1060&diff=2391072Sandbox Reserved 10602015-04-03T18:38:23Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==Your Heading Here (maybe something like 'Structure')==<br />
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
<br />
<scene name='69/694227/Arg_68_conformation_1/1'>Conformation 1</scene><br />
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<scene name='69/694227/Arg_68_conformation_2/1'>Conformation 2</scene><br />
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== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2390994Sandbox Reserved 10612015-04-03T17:23:39Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
This page is for Bryant Dawson and Kate Burke hehehe<br />
<br />
== Overview ==<br />
''Mycobacterium tuberculosis'' resides in the lungs of a host and upon becoming active, results in symptoms such as chest pains, weakness, and intense coughing. Left untreated and unmanaged, TB can lead to death (1.5 million in 2013). The disease has a high co-morbidity with HIV/AIDS due to its immunocompromising tendencies. Tuberculosis is one of the most heavily studied diseases today. With over 9 million infections worldwide per year, the necessity for antimicrobial agents to combat emerging multi-drug resistant strands is imperative. ''Mycobacterium tuberculosis'' NrdH is a small glutaredoxin-like protein involved in the electron transport chain that eventually leads to ribonucleotide reduction in tuberculosis. <br />
<br />
== Background ==<br />
<br />
MtNrdH has been identified as an electron carrier protein in ribonuleotide reduction. Ribonucleotide reduction uses an enzyme called ribonucleotide reductase (RNR) to make deoxyribonucleotides, which act as precursors to DNA synthesis. Three classes of RNRs have been identified; each class differs in cofactor requirement, structure, and oxygen dependence, but the general catalytic mechanism is conserved in all three classes. Mycobacterium tuberculosis uses class I ribonucleotide reductase. <br />
Class 1 RNR is further subdivided into class Ia and Ib. Both Ia and Ib reduce ribonucleotide 5’ diphosphate to deoxyribonucleotide 5’ diphosphate (NDP dNDP). After ribonucleotide reductase performs the first round of reduction, RNR must be reduced again to reset the cycle. In class Ib, RNR is reduced by either glutadoxin or thiordoxin, which are first reduced by glutadoxin reductase and thiordoxin reductase, respectively. In class Ib, RNR is reduced by NrdE, which is first reduced by NrdH. An important distinction between Ia and Ib is that Ia is present in eukaryotes, eubacteria, bacteriophages, and virus, but Ib is only present in eubacteria. <br />
<br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2388323Sandbox Reserved 10612015-03-27T18:37:57Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
== Structure of ''Mycobacterium Tuberculosis'' NrdH ==<br />
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
This page is for Bryant Dawson and Kate Burke hehehe<br />
<br />
== Background ==<br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Katelyn Burkehttps://proteopedia.org/index.php?title=Sandbox_Reserved_1061&diff=2388312Sandbox Reserved 10612015-03-27T18:31:02Z<p>Katelyn Burke: </p>
<hr />
<div>{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE --><br />
==Your Heading Here (maybe something like 'Structure')==<br />
<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''><br />
This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the &lt; and &gt; signs.<br />
You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.<br />
<br />
This page is for Bryant Dawson and Kate Burke hehehe<br />
<br />
== Background ==<br />
== Function ==<br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Katelyn Burkehttps://proteopedia.org/index.php?title=User:Katelyn_Burke/Sandbox_1&diff=2386157User:Katelyn Burke/Sandbox 12015-03-20T01:58:43Z<p>Katelyn Burke: </p>
<hr />
<div>==4HS1 structure==<br />
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[[Image:Super imposed molecules.png |200 px|left|thumb|Figure Legend ]]<br />
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This is the <scene name='69/696880/Secondary_structure_of_mtnrdh/1'>Secondary Structure</scene> of MtNrdH.<br />
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<Structure load='4HS1' size='350' frame='true' align='right' caption='4HS1' scene='Insert optional scene name here' /><br />
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== Function ==<br />
<br />
== Conserved Sequences ==<br />
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In red is the conserved sequence <scene name='69/696880/Cvqc/4'>CVQC</scene> where reduction occurs. <br />
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== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Katelyn Burkehttps://proteopedia.org/index.php?title=User:Katelyn_Burke/Sandbox_1&diff=2386121User:Katelyn Burke/Sandbox 12015-03-18T16:53:29Z<p>Katelyn Burke: </p>
<hr />
<div>==4HS1 structure==<br />
<br />
[[Image:Super imposed molecules.png |200 px|left|thumb|Figure Legend ]]<br />
<br />
This is the <scene name='69/696880/Secondary_structure_of_mtnrdh/1'>Secondary Structure</scene> of MtNrdH.<br />
<br />
<Structure load='4HS1' size='350' frame='true' align='right' caption='4HS1' scene='Insert optional scene name here' /><br />
<br />
== Function ==<br />
<br />
== Conserved Sequences ==<br />
<br />
In red is the conserved sequence <scene name='69/696880/Cvqc/4'>CVQC</scene> where reduction occurs. <br />
<br />
== Disease ==<br />
<br />
== Relevance ==<br />
<br />
== Structural highlights ==<br />
<br />
This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.<br />
<br />
</StructureSection><br />
== References ==<br />
<references/></div>Katelyn Burke