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[[Image:1wvg.gif|left|200px]]


{{Structure
==Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi==
|PDB= 1wvg |SIZE=350|CAPTION= <scene name='initialview01'>1wvg</scene>, resolution 1.8&Aring;
<StructureSection load='1wvg' size='340' side='right'caption='[[1wvg]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=APR:ADENOSINE-5-DIPHOSPHORIBOSE'>APR</scene> and <scene name='pdbligand=CXY:CYTIDINE-5'-DIPHOSPHO-BETA-D-XYLOSE'>CXY</scene>
<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>
|ACTIVITY= [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]  
</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>
|GENE= ddhB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90370 Salmonella enterica subsp. enterica serovar Typhi])
<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>
}}
<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>
 
</table>
'''Structure of CDP-D-glucose 4,6-dehydratase from Salmonella typhi'''
== Function ==
 
[https://www.uniprot.org/uniprot/RFBG_SALTY RFBG_SALTY]
 
== Evolutionary Conservation ==
==Overview==
[[Image:Consurf_key_small.gif|200px|right]]
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.
Check<jmol>
 
  <jmolCheckbox>
==About this Structure==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wv/1wvg_consurf.spt"</scriptWhenChecked>
1WVG is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_typhi Salmonella enterica subsp. enterica serovar typhi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WVG OCA].  
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==Reference==
  </jmolCheckbox>
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://www.ncbi.nlm.nih.gov/pubmed/15805590 15805590]
</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].
[[Category: CDP-glucose 4,6-dehydratase]]
<div style="clear:both"></div>
[[Category: Salmonella enterica subsp. enterica serovar typhi]]
__TOC__
[[Category: Single protein]]
</StructureSection>
[[Category: Holden, H M.]]
[[Category: Large Structures]]
[[Category: Koropatkin, N M.]]
[[Category: Salmonella enterica subsp. enterica serovar Typhi str. CT18]]
[[Category: APR]]
[[Category: Holden HM]]
[[Category: CXY]]
[[Category: Koropatkin NM]]
[[Category: rossmann fold]]
[[Category: short-chain dehydrogenase/reductase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 15:02:00 2008''

Latest revision as of 13:34, 13 March 2024

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

1wvg, resolution 1.80Å

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