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| | <StructureSection load='1ker' size='340' side='right'caption='[[1ker]], [[Resolution|resolution]] 2.20Å' scene=''> | | <StructureSection load='1ker' size='340' side='right'caption='[[1ker]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1ker]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_43765 Atcc 43765]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KER OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1KER FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1ker]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_suis Streptococcus suis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KER OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KER FirstGlance]. <br> |
| - | </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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1kep|1kep]], [[1ket|1ket]], [[1keu|1keu]], [[1kew|1kew]], [[1g1a|1g1a]]</div></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>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rmlB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1307 ATCC 43765])</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=1ker FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ker OCA], [https://pdbe.org/1ker PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ker RCSB], [https://www.ebi.ac.uk/pdbsum/1ker PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ker ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dTDP-glucose_4,6-dehydratase dTDP-glucose 4,6-dehydratase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.46 4.2.1.46] </span></td></tr> | + | |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1ker FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ker OCA], [http://pdbe.org/1ker PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ker RCSB], [http://www.ebi.ac.uk/pdbsum/1ker PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ker ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RMLB_STRMU RMLB_STRMU]] 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 (By similarity). | + | [https://www.uniprot.org/uniprot/Q8GIP9_STRSU Q8GIP9_STRSU] |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 43765]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: DTDP-glucose 4,6-dehydratase]] | + | [[Category: Streptococcus suis]] |
| - | [[Category: Allard, S T.M]] | + | [[Category: Allard STM]] |
| - | [[Category: Allen, A G]] | + | [[Category: Allen AG]] |
| - | [[Category: Beis, K]] | + | [[Category: Beis K]] |
| - | [[Category: Giraud, M F]] | + | [[Category: Giraud M-F]] |
| - | [[Category: Graninger, M]] | + | [[Category: Graninger M]] |
| - | [[Category: Gross, J W]] | + | [[Category: Gross JW]] |
| - | [[Category: Hegeman, A D]] | + | [[Category: Hegeman AD]] |
| - | [[Category: Messner, P]] | + | [[Category: Messner P]] |
| - | [[Category: Naismith, J H]] | + | [[Category: Naismith JH]] |
| - | [[Category: Whitfield, C]] | + | [[Category: Whitfield C]] |
| - | [[Category: Lyase]]
| + | |
| - | [[Category: Rossmann fold]]
| + | |
| Structural highlights
Function
Q8GIP9_STRSU
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Allard ST, Beis K, Giraud MF, Hegeman AD, Gross JW, Wilmouth RC, Whitfield C, Graninger M, Messner P, Allen AG, Maskell DJ, Naismith JH. Toward a structural understanding of the dehydratase mechanism. Structure. 2002 Jan;10(1):81-92. PMID:11796113
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