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2gh4

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Revision as of 07:16, 20 June 2018

YteR/D143N/dGalA-Rha

Structural highlights

2gh4 is a 1 chain structure with sequence from "vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
Gene:	yteR ("Vibrio subtilis" Ehrenberg 1835)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[URHG2_BACSU] Catalyzes the hydrolysis of unsaturated rhamnogalacturonan disaccharide to yield unsaturated D-galacturonic acid and L-rhamnose. It cannot act on unsaturated glucuronyl hydrolase (UGL) substrates containing unsaturated D-glucuronic acid at the non-reducing terminus, although the active pockets of YesR and UGL are very similar.^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Bacillus subtilis strain 168 YteR has been identified as a novel enzyme "unsaturated rhamnogalacturonyl hydrolase" classified in glycoside hydrolase family 105. This enzyme acts specifically on unsaturated rhamnogalacturonan (RG) produced from plant cell wall RG type-I treated with RG lyases, releasing unsaturated galacturonic acid (DeltaGalA) from the substrate. The most likely candidate catalytic residue is Asp-143. Here, we show the structure of D143N in complex with unsaturated RG disaccharide (substrate) determined at 1.9A resolution by X-ray crystallography. This structural feature directly contributes to the postulation of the enzyme reaction mechanism. YteR triggers the hydration of vinyl ether group in DeltaGalA, but not of glycoside bond, by using Asp-143 as a general acid and base catalyst. Asp-143 donates proton to the double bond of DeltaGalA as an acid catalyst and also deprotonates a water molecule as a base catalyst. Deprotonated water molecule attacks the C5 atom of DeltaGalA.

Structure of unsaturated rhamnogalacturonyl hydrolase complexed with substrate.,Itoh T, Ochiai A, Mikami B, Hashimoto W, Murata K Biochem Biophys Res Commun. 2006 Sep 8;347(4):1021-9. Epub 2006 Jul 17. PMID:16870154^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Itoh T, Ochiai A, Mikami B, Hashimoto W, Murata K. A novel glycoside hydrolase family 105: the structure of family 105 unsaturated rhamnogalacturonyl hydrolase complexed with a disaccharide in comparison with family 88 enzyme complexed with the disaccharide. J Mol Biol. 2006 Jul 14;360(3):573-85. Epub 2006 May 9. PMID:16781735 doi:10.1016/j.jmb.2006.04.047
↑ Itoh T, Ochiai A, Mikami B, Hashimoto W, Murata K. Structure of unsaturated rhamnogalacturonyl hydrolase complexed with substrate. Biochem Biophys Res Commun. 2006 Sep 8;347(4):1021-9. Epub 2006 Jul 17. PMID:16870154 doi:10.1016/j.bbrc.2006.07.034

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2gh4"

@@ Line 1: / Line 1: @@
 ==YteR/D143N/dGalA-Rha==
 <StructureSection load='2gh4' size='340' side='right' caption='[[2gh4]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2gh4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GH4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GH4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2gh4]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GH4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2GH4 FirstGlance]. <br>
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GAD:2,6-ANHYDRO-3-DEOXY-D-ERYTHRO-HEX-2-ENONIC+ACID'>GAD</scene>, <scene name='pdbligand=RAM:ALPHA-L-RHAMNOSE'>RAM</scene></td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yteR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yteR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Vibrio subtilis" Ehrenberg 1835])</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2gh4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gh4 OCA], [http://pdbe.org/2gh4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gh4 RCSB], [http://www.ebi.ac.uk/pdbsum/2gh4 PDBsum]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2gh4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gh4 OCA], [http://pdbe.org/2gh4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2gh4 RCSB], [http://www.ebi.ac.uk/pdbsum/2gh4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2gh4 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 13: / Line 14: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gh/2gh4_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/gh/2gh4_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 32: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Bacillus globigii migula 1900]]
+[[Category: Vibrio subtilis ehrenberg 1835]]
 [[Category: Hashimoto, W]]
 [[Category: Itoh, T]]

2gh4

From Proteopedia

Revision as of 07:16, 20 June 2018

YteR/D143N/dGalA-Rha

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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