1ker: Difference between revisions
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== 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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KER FirstGlance]. <br> | <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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KER FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kep|1kep]], [[1ket|1ket]], [[1keu|1keu]], [[1kew|1kew]], [[1g1a|1g1a]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kep|1kep]], [[1ket|1ket]], [[1keu|1keu]], [[1kew|1kew]], [[1g1a|1g1a]]</td></tr> | ||
<tr><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='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><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='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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ker FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ker OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ker RCSB], [http://www.ebi.ac.uk/pdbsum/1ker PDBsum]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ker FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ker OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ker RCSB], [http://www.ebi.ac.uk/pdbsum/1ker PDBsum]</span></td></tr> | ||
<table> | </table> | ||
== 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). | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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[[Category: Atcc 43765]] | [[Category: Atcc 43765]] | ||
[[Category: DTDP-glucose 4,6-dehydratase]] | [[Category: DTDP-glucose 4,6-dehydratase]] | ||
[[Category: Allard, S T.M | [[Category: Allard, S T.M]] | ||
[[Category: Allen, A G | [[Category: Allen, A G]] | ||
[[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, J W]] | ||
[[Category: Hegeman, A D | [[Category: Hegeman, A D]] | ||
[[Category: Messner, P | [[Category: Messner, P]] | ||
[[Category: Naismith, J H | [[Category: Naismith, J H]] | ||
[[Category: Whitfield, C | [[Category: Whitfield, C]] | ||
[[Category: Lyase]] | [[Category: Lyase]] | ||
[[Category: Rossmann fold]] | [[Category: Rossmann fold]] | ||
Revision as of 10:58, 25 December 2014
The crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with dTDP-D-glucose boundThe crystal structure of dTDP-D-glucose 4,6-dehydratase (RmlB) from Streptococcus suis with dTDP-D-glucose bound
Structural highlights
Function[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). 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 PubMeddTDP-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. References |
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