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| - | [[Image:1rkx.gif|left|200px]] | |
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| - | {{Structure
| + | ==Crystal Structure at 1.8 Angstrom of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis== |
| - | |PDB= 1rkx |SIZE=350|CAPTION= <scene name='initialview01'>1rkx</scene>, resolution 1.80Å
| + | <StructureSection load='1rkx' size='340' side='right'caption='[[1rkx]], [[Resolution|resolution]] 1.80Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>
| + | <table><tr><td colspan='2'>[[1rkx]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Yersinia_pseudotuberculosis Yersinia pseudotuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RKX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RKX FirstGlance]. <br> |
| - | |ACTIVITY= <span class='plainlinks'>[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] </span>
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</td></tr> |
| - | |GENE= ascB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=633 Yersinia pseudotuberculosis])
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene></td></tr> |
| - | |DOMAIN=
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rkx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rkx OCA], [https://pdbe.org/1rkx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rkx RCSB], [https://www.ebi.ac.uk/pdbsum/1rkx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rkx ProSAT]</span></td></tr> |
| - | |RELATEDENTRY= | + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1rkx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rkx OCA], [http://www.ebi.ac.uk/pdbsum/1rkx PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1rkx RCSB]</span>
| + | == Function == |
| - | }}
| + | [https://www.uniprot.org/uniprot/Q57329_YERPU Q57329_YERPU] |
| - | | + | == Evolutionary Conservation == |
| - | '''Crystal Structure at 1.8 Angstrom of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis'''
| + | [[Image:Consurf_key_small.gif|200px|right]] |
| - | | + | Check<jmol> |
| - | | + | <jmolCheckbox> |
| - | ==Overview== | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/rk/1rkx_consurf.spt"</scriptWhenChecked> |
| - | CDP-D-glucose 4,6-dehydratase catalyzes the conversion of CDP-D-glucose to CDP-4-keto-6-deoxyglucose in an NAD(+)-dependent manner. The product of this conversion is a building block for a variety of primary antigenic determinants in bacteria, possibly implicated directly in reactive arthritis. Here, we describe the solution of the high-resolution crystal structure of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis in the resting state. This structure represents the first CDP nucleotide utilizing dehydratase of the short-chain dehydrogenase/reductase (SDR) family to be determined, as well as the first tetrameric structure of the subfamily of SDR enzymes in which NAD(+) undergoes a full reaction cycle. On the basis of a comparison of this structure with structures of homologous enzymes, a chemical mechanism is proposed in which Tyr157 acts as the catalytic base, initiating hydride transfer by abstraction of the proton from the sugar 4'-hydroxyl. Concomitant with the removal of the proton from the 4'-hydroxyl oxygen, the sugar 4'-hydride is transferred to the B face of the NAD(+) cofactor, forming the reduced cofactor and a CDP-4-keto-d-glucose intermediate. A conserved Lys161 most likely acts to position the NAD(+) cofactor so that hydride transfer is favorable and/or to reduce the pK(a) of Tyr157. Following substrate oxidation, we propose that Lys134, acting as a base, would abstract the 5'-hydrogen of CDP-4-keto-D-glucose, priming the intermediate for the spontaneous loss of water. Finally, the resulting Delta(5,6)-glucoseen intermediate would be reduced suprafacially by the cofactor, and reprotonation at C-5' is likely mediated by Lys134.
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> |
| - | | + | <text>to colour the structure by Evolutionary Conservation</text> |
| - | ==About this Structure== | + | </jmolCheckbox> |
| - | 1RKX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Yersinia_pseudotuberculosis Yersinia pseudotuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RKX OCA].
| + | </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=1rkx ConSurf]. |
| - | | + | <div style="clear:both"></div> |
| - | ==Reference==
| + | __TOC__ |
| - | Crystal structure at 1.8 A resolution of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis., Vogan EM, Bellamacina C, He X, Liu HW, Ringe D, Petsko GA, Biochemistry. 2004 Mar 23;43(11):3057-67. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15023057 15023057]
| + | </StructureSection> |
| - | [[Category: CDP-glucose 4,6-dehydratase]]
| + | [[Category: Large Structures]] |
| - | [[Category: Single protein]] | + | |
| | [[Category: Yersinia pseudotuberculosis]] | | [[Category: Yersinia pseudotuberculosis]] |
| - | [[Category: Bellamacina, C.]] | + | [[Category: Bellamacina C]] |
| - | [[Category: He, X.]] | + | [[Category: He X]] |
| - | [[Category: Liu, H W.]] | + | [[Category: Liu HW]] |
| - | [[Category: Petsko, G A.]] | + | [[Category: Petsko GA]] |
| - | [[Category: Ringe, D.]] | + | [[Category: Ringe D]] |
| - | [[Category: Vogan, E M.]] | + | [[Category: Vogan EM]] |
| - | [[Category: cdp glucose dehydratase]]
| + | |
| - | [[Category: dehydratase]]
| + | |
| - | [[Category: sdr]]
| + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 23:29:36 2008''
| + | |
