1keu
From Proteopedia
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| - | {{STRUCTURE_1keu| PDB=1keu | SCENE= }} | ||
| - | ===The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Salmonella enterica serovar Typhimurium with dTDP-D-glucose bound=== | ||
| - | {{ABSTRACT_PUBMED_11796113}} | ||
| - | == | + | ==The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Salmonella enterica serovar Typhimurium with dTDP-D-glucose bound== |
| - | [[http://www.uniprot.org/uniprot/ | + | <StructureSection load='1keu' size='340' side='right'caption='[[1keu]], [[Resolution|resolution]] 2.40Å' scene=''> |
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[1keu]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Salmonella_enterica_subsp._enterica_serovar_Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KEU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KEU FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAU:2DEOXY-THYMIDINE-5-DIPHOSPHO-ALPHA-D-GLUCOSE'>DAU</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</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=1keu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1keu OCA], [https://pdbe.org/1keu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1keu RCSB], [https://www.ebi.ac.uk/pdbsum/1keu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1keu ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/RMLB_SALTY RMLB_SALTY] Catalyzes the dehydration of dTDP-D-glucose to form dTDP-6-deoxy-D-xylo-4-hexulose via a three-step process involving oxidation, dehydration and reduction.<ref>PMID:11796113</ref> | ||
| + | == Evolutionary Conservation == | ||
| + | [[Image:Consurf_key_small.gif|200px|right]] | ||
| + | Check<jmol> | ||
| + | <jmolCheckbox> | ||
| + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ke/1keu_consurf.spt"</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
| + | <text>to colour the structure by Evolutionary Conservation</text> | ||
| + | </jmolCheckbox> | ||
| + | </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=1keu ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
| + | dTDP-D-glucose 4,6-dehydratase (RmlB) was first identified in the L-rhamnose biosynthetic pathway, where it catalyzes the conversion of dTDP-D-glucose into dTDP-4-keto-6-deoxy-D-glucose. The structures of RmlB from Salmonella enterica serovar Typhimurium in complex with substrate deoxythymidine 5'-diphospho-D-glucose (dTDP-D-glucose) and deoxythymidine 5'-diphosphate (dTDP), and RmlB from Streptococcus suis serotype 2 in complex with dTDP-D-glucose, dTDP, and deoxythymidine 5'-diphospho-D-pyrano-xylose (dTDP-xylose) have all been solved at resolutions between 1.8 A and 2.4 A. The structures show that the active sites are highly conserved. Importantly, the structures show that the active site tyrosine functions directly as the active site base, and an aspartic and glutamic acid pairing accomplishes the dehydration step of the enzyme mechanism. We conclude that the substrate is required to move within the active site to complete the catalytic cycle and that this movement is driven by the elimination of water. The results provide insight into members of the SDR superfamily. | ||
| - | + | Toward a structural understanding of the dehydratase mechanism.,Allard ST, Beis K, Giraud MF, Hegeman AD, Gross JW, Wilmouth RC, Whitfield C, Graninger M, Messner P, Allen AG, Maskell DJ, Naismith JH Structure. 2002 Jan;10(1):81-92. PMID:11796113<ref>PMID:11796113</ref> | |
| - | + | ||
| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | < | + | </div> |
| - | [[Category: | + | <div class="pdbe-citations 1keu" style="background-color:#fffaf0;"></div> |
| - | [[Category: | + | |
| - | [[Category: Allard | + | ==See Also== |
| - | [[Category: Allen | + | *[[DTDP-glucose 4%2C6-dehydratase|DTDP-glucose 4%2C6-dehydratase]] |
| - | [[Category: Beis | + | == References == |
| - | [[Category: Giraud | + | <references/> |
| - | [[Category: Graninger | + | __TOC__ |
| - | [[Category: Gross | + | </StructureSection> |
| - | [[Category: Hegeman | + | [[Category: Large Structures]] |
| - | [[Category: Messner | + | [[Category: Salmonella enterica subsp. enterica serovar Typhimurium]] |
| - | [[Category: Naismith | + | [[Category: Allard STM]] |
| - | [[Category: Whitfield | + | [[Category: Allen AG]] |
| - | + | [[Category: Beis K]] | |
| - | + | [[Category: Giraud M-F]] | |
| + | [[Category: Graninger M]] | ||
| + | [[Category: Gross JW]] | ||
| + | [[Category: Hegeman AD]] | ||
| + | [[Category: Messner P]] | ||
| + | [[Category: Naismith JH]] | ||
| + | [[Category: Whitfield C]] | ||
Current revision
The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Salmonella enterica serovar Typhimurium with dTDP-D-glucose bound
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