2d8l

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(New page: 200px<br /><applet load="2d8l" size="450" color="white" frame="true" align="right" spinBox="true" caption="2d8l, resolution 1.70&Aring;" /> '''Crystal Structure of...)
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[[Image:2d8l.gif|left|200px]]<br /><applet load="2d8l" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="2d8l, resolution 1.70&Aring;" />
 
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'''Crystal Structure of Unsaturated Rhamnogalacturonyl Hydrolase in complex with dGlcA-GalNAc'''<br />
 
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==Overview==
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==Crystal Structure of Unsaturated Rhamnogalacturonyl Hydrolase in complex with dGlcA-GalNAc==
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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.
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<StructureSection load='2d8l' size='340' side='right'caption='[[2d8l]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[2d8l]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2D8L OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2D8L FirstGlance]. <br>
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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].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GCD:4,5-DEHYDRO-D-GLUCURONIC+ACID'>GCD</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene>, <scene name='pdbligand=PRD_900058:UNSATURATED+CHONDROITIN+DISACCHARIDE'>PRD_900058</scene></td></tr>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2d8l FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2d8l OCA], [https://pdbe.org/2d8l PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2d8l RCSB], [https://www.ebi.ac.uk/pdbsum/2d8l PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2d8l ProSAT]</span></td></tr>
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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., Itoh T, Ochiai A, Mikami B, Hashimoto W, Murata K, J Mol Biol. 2006 Jul 14;360(3):573-85. Epub 2006 May 9. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16781735 16781735]
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</table>
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== Function ==
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[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>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/d8/2d8l_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2d8l ConSurf].
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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Bacillus subtilis]]
[[Category: Bacillus subtilis]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Hashimoto, W.]]
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[[Category: Hashimoto W]]
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[[Category: Itoh, T.]]
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[[Category: Itoh T]]
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[[Category: Mikami, B.]]
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[[Category: Mikami B]]
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[[Category: Murata, K.]]
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[[Category: Murata K]]
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[[Category: Ochiai, A.]]
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[[Category: Ochiai A]]
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[[Category: UCD]]
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[[Category: unsaturated rhamnogalacturonyl hydrolase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 09:29:14 2007''
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Current revision

Crystal Structure of Unsaturated Rhamnogalacturonyl Hydrolase in complex with dGlcA-GalNAc

PDB ID 2d8l

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