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| | ==YteR/D143N/dGalA-Rha== | | ==YteR/D143N/dGalA-Rha== |
| - | <StructureSection load='2gh4' size='340' side='right' caption='[[2gh4]], [[Resolution|resolution]] 1.90Å' scene=''> | + | <StructureSection load='2gh4' size='340' side='right'caption='[[2gh4]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <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> | + | <table><tr><td colspan='2'>[[2gh4]] is a 1 chain structure with sequence from [https://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 [https://proteopedia.org/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> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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 "Vibrio subtilis" Ehrenberg 1835])</td></tr> | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">yteR ([https://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], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2gh4 ProSAT]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2gh4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gh4 OCA], [https://pdbe.org/2gh4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gh4 RCSB], [https://www.ebi.ac.uk/pdbsum/2gh4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gh4 ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/URHG2_BACSU 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.<ref>PMID:16781735</ref> | + | [[https://www.uniprot.org/uniprot/URHG2_BACSU 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.<ref>PMID:16781735</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Vibrio subtilis ehrenberg 1835]] | | [[Category: Vibrio subtilis ehrenberg 1835]] |
| | + | [[Category: Large Structures]] |
| | [[Category: Hashimoto, W]] | | [[Category: Hashimoto, W]] |
| | [[Category: Itoh, T]] | | [[Category: Itoh, T]] |
| Structural highlights
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
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