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1rkx

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[[Image:1rkx.gif|left|200px]]<br /><applet load="1rkx" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1rkx, resolution 1.80&Aring;" />
 
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'''Crystal Structure at 1.8 Angstrom of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis'''<br />
 
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==Overview==
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==Crystal Structure at 1.8 Angstrom of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis==
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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.
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<StructureSection load='1rkx' size='340' side='right'caption='[[1rkx]], [[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'>[[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>
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1RKX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Yersinia_pseudotuberculosis Yersinia pseudotuberculosis] with <scene name='pdbligand=NAD:'>NAD</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1RKX 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=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=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>
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=15023057 15023057]
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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: Single protein]]
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[https://www.uniprot.org/uniprot/Q57329_YERPU Q57329_YERPU]
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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/rk/1rkx_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=1rkx 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]]
[[Category: Yersinia pseudotuberculosis]]
[[Category: Yersinia pseudotuberculosis]]
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[[Category: Bellamacina, C.]]
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[[Category: Bellamacina C]]
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[[Category: He, X.]]
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[[Category: He X]]
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[[Category: Liu, H W.]]
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[[Category: Liu HW]]
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[[Category: Petsko, G A.]]
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[[Category: Petsko GA]]
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[[Category: Ringe, D.]]
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[[Category: Ringe D]]
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[[Category: Vogan, E M.]]
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[[Category: Vogan EM]]
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[[Category: NAD]]
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[[Category: cdp glucose dehydratase]]
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[[Category: dehydratase]]
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[[Category: sdr]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:51:59 2008''
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Current revision

Crystal Structure at 1.8 Angstrom of CDP-D-glucose 4,6-dehydratase from Yersinia pseudotuberculosis

PDB ID 1rkx

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