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1wvg

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(New page: 200px<br /><applet load="1wvg" size="450" color="white" frame="true" align="right" spinBox="true" caption="1wvg, resolution 1.8&Aring;" /> '''Structure of CDP-D-gl...)
Current revision (13:34, 13 March 2024) (edit) (undo)
 
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[[Image:1wvg.gif|left|200px]]<br /><applet load="1wvg" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1wvg, resolution 1.8&Aring;" />
 
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'''Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi'''<br />
 
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==Overview==
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==Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi==
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Tyvelose is a unique 3,6-dideoxyhexose found in the O antigens of some, pathogenic species of Yersinia and Salmonella. It is produced via a, complex biochemical pathway that employs CDP-D-glucose as the starting, ligand. CDP-D-glucose 4,6-dehydratase catalyzes the first irreversible, step in the synthesis of this 3,6-dideoxysugar by converting CDP-D-glucose, to CDP-4-keto-6-deoxyglucose via an NAD+ -dependent intramolecular, oxidation-reduction reaction. Here, the cloning, protein purification and, X-ray crystallographic analysis of CDP-D-glucose 4,6-dehydratase from, Salmonella typhi complexed with the substrate analog CDP-D-xylose are, described. Each subunit of the tetrameric enzyme folds into two domains., The N-terminal region contains a Rossmann fold and provides the platform, for NAD(H) binding. The C-terminal motif is primarily composed of, alpha-helices and houses the binding pocket for the CDP portion of the, CDP-D-xylose ligand. The xylose moiety extends into the active-site cleft, that is located between the two domains. Key residues involved in, anchoring the sugar group to the protein include Ser134, Tyr159, Asn197, and Arg208. Strikingly, Ser134 O gamma and Tyr159 O eta sit within 2.9 A, of the 4'-hydroxyl group of xylose. Additionally, the side chains of, Asp135 and Lys136 are located at 3.5 and 3.2 A, respectively, from C-5 of, xylose. In the structurally related dTDP-D-glucose 4,6-dehydratase, the, Asp/Lys pair is replaced with an Asp/Glu couple. On the basis of this, investigation, it can be speculated that Tyr159 serves as the catalytic, base to abstract the 4'-hydroxyl proton from the sugar and that Asp135 and, Lys136 play critical roles in the subsequent dehydration step that leads, to the final product.
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<StructureSection load='1wvg' size='340' side='right'caption='[[1wvg]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1wvg]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhi_str._CT18 Salmonella enterica subsp. enterica serovar Typhi str. CT18]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WVG OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WVG FirstGlance]. <br>
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1WVG is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhi Salmonella enterica subsp. enterica serovar typhi] with APR and CXY as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/CDP-glucose_4,6-dehydratase CDP-glucose 4,6-dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.45 4.2.1.45] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1WVG 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]] 1.8&#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=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene>, <scene name='pdbligand=CXY:CYTIDINE-5-DIPHOSPHO-BETA-D-XYLOSE'>CXY</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=1wvg FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wvg OCA], [https://pdbe.org/1wvg PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wvg RCSB], [https://www.ebi.ac.uk/pdbsum/1wvg PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wvg ProSAT]</span></td></tr>
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Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi complexed with CDP-D-xylose., Koropatkin NM, Holden HM, Acta Crystallogr D Biol Crystallogr. 2005 Apr;61(Pt 4):365-73. Epub 2005, Mar 24. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15805590 15805590]
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</table>
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[[Category: CDP-glucose 4,6-dehydratase]]
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== Function ==
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[[Category: Salmonella enterica subsp. enterica serovar typhi]]
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[https://www.uniprot.org/uniprot/RFBG_SALTY RFBG_SALTY]
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[[Category: Single protein]]
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== Evolutionary Conservation ==
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[[Category: Holden, H.M.]]
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[[Image:Consurf_key_small.gif|200px|right]]
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[[Category: Koropatkin, N.M.]]
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Check<jmol>
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[[Category: APR]]
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<jmolCheckbox>
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[[Category: CXY]]
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wv/1wvg_consurf.spt"</scriptWhenChecked>
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[[Category: rossmann fold]]
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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[[Category: short-chain dehydrogenase/reductase]]
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 05:42:05 2007''
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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=1wvg ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Salmonella enterica subsp. enterica serovar Typhi str. CT18]]
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[[Category: Holden HM]]
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[[Category: Koropatkin NM]]

Current revision

Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi

PDB ID 1wvg

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