2d8l: Difference between revisions

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[[Image:2d8l.gif|left|200px]]<br /><applet load="2d8l" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

[[Image:2d8l.gif|left|200px]]<br /><applet load="2d8l" size="350" color="white" frame="true" align="right" spinBox="true"

caption="2d8l, resolution 1.70Å" />

'''Crystal Structure of Unsaturated Rhamnogalacturonyl Hydrolase in complex with dGlcA-GalNAc'''<br />

==Overview==

YteR, a hypothetical protein with unknown functions, is derived from, Bacillus subtilis strain 168 and has an overall structure similar to that, of bacterial unsaturated glucuronyl hydrolase (UGL), although it exhibits, little amino acid sequence identity with UGL. UGL releases unsaturated, glucuronic acid from glycosaminoglycan treated with glycosaminoglycan, lyases. The amino acid sequence of YteR shows a significant homology (26%, identity) with the hypothetical protein YesR also from B. subtilis strain, 168. To clarify the intrinsic functions of YteR and YesR, both proteins, were overexpressed in Escherichia coli, purified, and characterized. Based, on their gene arrangements in genome and enzyme properties, YteR and YesR, were found to constitute a novel enzyme activity, "unsaturated, rhamnogalacturonyl hydrolase," classified as new glycoside hydrolase, family 105. This enzyme acts specifically on unsaturated, rhamnogalacturonan (RG) obtained from RG type-I treated with RG lyases and, releases an unsaturated galacturonic acid. The crystal structure of YteR, complexed with unsaturated chondroitin disaccharide (UGL substrate) was, obtained and compared to the structure of UGL complexed with the same, disaccharide. The UGL substrate is sterically hindered with the active, pocket of YteR. The protruding loop of YteR prevents the UGL substrate, from being bound effectively. The most likely candidate catalytic residues, for general acid/base are Asp143 in YteR and Asp135 in YesR. This is, supported by three-dimensional structural and site-directed mutagenesis, studies. These findings provide molecular insights into novel enzyme, catalysis and sequential reaction mechanisms involved in RG-I, depolymerization by bacteria.

YteR, a hypothetical protein with unknown functions, is derived from Bacillus subtilis strain 168 and has an overall structure similar to that of bacterial unsaturated glucuronyl hydrolase (UGL), although it exhibits little amino acid sequence identity with UGL. UGL releases unsaturated glucuronic acid from glycosaminoglycan treated with glycosaminoglycan lyases. The amino acid sequence of YteR shows a significant homology (26% identity) with the hypothetical protein YesR also from B. subtilis strain 168. To clarify the intrinsic functions of YteR and YesR, both proteins were overexpressed in Escherichia coli, purified, and characterized. Based on their gene arrangements in genome and enzyme properties, YteR and YesR were found to constitute a novel enzyme activity, "unsaturated rhamnogalacturonyl hydrolase," classified as new glycoside hydrolase family 105. This enzyme acts specifically on unsaturated rhamnogalacturonan (RG) obtained from RG type-I treated with RG lyases and releases an unsaturated galacturonic acid. The crystal structure of YteR complexed with unsaturated chondroitin disaccharide (UGL substrate) was obtained and compared to the structure of UGL complexed with the same disaccharide. The UGL substrate is sterically hindered with the active pocket of YteR. The protruding loop of YteR prevents the UGL substrate from being bound effectively. The most likely candidate catalytic residues for general acid/base are Asp143 in YteR and Asp135 in YesR. This is supported by three-dimensional structural and site-directed mutagenesis studies. These findings provide molecular insights into novel enzyme catalysis and sequential reaction mechanisms involved in RG-I depolymerization by bacteria.

==About this Structure==

2D8L is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with UCD as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=2D8L OCA].

2D8L is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with <scene name='pdbligand=UCD:'>UCD</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D8L OCA].

==Reference==

Line 21:

[[Category: unsaturated rhamnogalacturonyl hydrolase]]

''Page seeded by [http://~~ispc~~.weizmann.ac.il/oca OCA ] on ~~Wed Nov~~ 21 09:29:~~14 2007~~''

''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:56:12 2008''

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@@ Line 1: / Line 1: @@
-[[Image:2d8l.gif|left|200px]]<br /><applet load="2d8l" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:2d8l.gif|left|200px]]<br /><applet load="2d8l" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="2d8l, resolution 1.70&Aring;" />
 '''Crystal Structure of Unsaturated Rhamnogalacturonyl Hydrolase in complex with dGlcA-GalNAc'''<br />
 ==Overview==
-YteR, a hypothetical protein with unknown functions, is derived from, Bacillus subtilis strain 168 and has an overall structure similar to that, of bacterial unsaturated glucuronyl hydrolase (UGL), although it exhibits, little amino acid sequence identity with UGL. UGL releases unsaturated, glucuronic acid from glycosaminoglycan treated with glycosaminoglycan, lyases. The amino acid sequence of YteR shows a significant homology (26%, identity) with the hypothetical protein YesR also from B. subtilis strain, 168. To clarify the intrinsic functions of YteR and YesR, both proteins, were overexpressed in Escherichia coli, purified, and characterized. Based, on their gene arrangements in genome and enzyme properties, YteR and YesR, were found to constitute a novel enzyme activity, "unsaturated, rhamnogalacturonyl hydrolase," classified as new glycoside hydrolase, family 105. This enzyme acts specifically on unsaturated, rhamnogalacturonan (RG) obtained from RG type-I treated with RG lyases and, releases an unsaturated galacturonic acid. The crystal structure of YteR, complexed with unsaturated chondroitin disaccharide (UGL substrate) was, obtained and compared to the structure of UGL complexed with the same, disaccharide. The UGL substrate is sterically hindered with the active, pocket of YteR. The protruding loop of YteR prevents the UGL substrate, from being bound effectively. The most likely candidate catalytic residues, for general acid/base are Asp143 in YteR and Asp135 in YesR. This is, supported by three-dimensional structural and site-directed mutagenesis, studies. These findings provide molecular insights into novel enzyme, catalysis and sequential reaction mechanisms involved in RG-I, depolymerization by bacteria.
+YteR, a hypothetical protein with unknown functions, is derived from Bacillus subtilis strain 168 and has an overall structure similar to that of bacterial unsaturated glucuronyl hydrolase (UGL), although it exhibits little amino acid sequence identity with UGL. UGL releases unsaturated glucuronic acid from glycosaminoglycan treated with glycosaminoglycan lyases. The amino acid sequence of YteR shows a significant homology (26% identity) with the hypothetical protein YesR also from B. subtilis strain 168. To clarify the intrinsic functions of YteR and YesR, both proteins were overexpressed in Escherichia coli, purified, and characterized. Based on their gene arrangements in genome and enzyme properties, YteR and YesR were found to constitute a novel enzyme activity, "unsaturated rhamnogalacturonyl hydrolase," classified as new glycoside hydrolase family 105. This enzyme acts specifically on unsaturated rhamnogalacturonan (RG) obtained from RG type-I treated with RG lyases and releases an unsaturated galacturonic acid. The crystal structure of YteR complexed with unsaturated chondroitin disaccharide (UGL substrate) was obtained and compared to the structure of UGL complexed with the same disaccharide. The UGL substrate is sterically hindered with the active pocket of YteR. The protruding loop of YteR prevents the UGL substrate from being bound effectively. The most likely candidate catalytic residues for general acid/base are Asp143 in YteR and Asp135 in YesR. This is supported by three-dimensional structural and site-directed mutagenesis studies. These findings provide molecular insights into novel enzyme catalysis and sequential reaction mechanisms involved in RG-I depolymerization by bacteria.
 ==About this Structure==
-D8L is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with UCD as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2D8L OCA].
+D8L is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with <scene name='pdbligand=UCD:'>UCD</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D8L OCA].
 ==Reference==
@@ Line 21: / Line 21: @@
 [[Category: unsaturated rhamnogalacturonyl hydrolase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 09:29:14 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:56:12 2008''