1kc3: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1kc3]] is a 1 chain structure with sequence from [http://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=1KC3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KC3 FirstGlance]. <br> | <table><tr><td colspan='2'>[[1kc3]] is a 1 chain structure with sequence from [http://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=1KC3 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1KC3 FirstGlance]. <br> | ||
</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=TRH:2-DEOXY-THYMIDINE-BETA-L-RHAMNOSE'>TRH</scene>< | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>, <scene name='pdbligand=TRH:2-DEOXY-THYMIDINE-BETA-L-RHAMNOSE'>TRH</scene></td></tr> | ||
<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kbz|1kbz]], [[1kc0|1kc0]], [[1kc1|1kc1]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1kbz|1kbz]], [[1kc0|1kc0]], [[1kc1|1kc1]]</td></tr> | ||
<tr><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rfbA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 Salmonella enterica subsp. enterica serovar Typhimurium])</td></tr> | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">rfbA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=90371 Salmonella enterica subsp. enterica serovar Typhimurium])</td></tr> | ||
<tr><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/dTDP-4-dehydrorhamnose_reductase dTDP-4-dehydrorhamnose reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.133 1.1.1.133] </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-4-dehydrorhamnose_reductase dTDP-4-dehydrorhamnose reductase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.133 1.1.1.133] </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=1kc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kc3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kc3 RCSB], [http://www.ebi.ac.uk/pdbsum/1kc3 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=1kc3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1kc3 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1kc3 RCSB], [http://www.ebi.ac.uk/pdbsum/1kc3 PDBsum]</span></td></tr> | ||
<table> | </table> | ||
== Function == | |||
[[http://www.uniprot.org/uniprot/RFBD_SALTY RFBD_SALTY]] Catalyzes the reduction of dTDP-6-deoxy-L-lyxo-4-hexulose to yield dTDP-L-rhamnose. RmlD uses NADH and NADPH nearly equally well. | |||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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[[Category: Salmonella enterica subsp. enterica serovar typhimurium]] | [[Category: Salmonella enterica subsp. enterica serovar typhimurium]] | ||
[[Category: DTDP-4-dehydrorhamnose reductase]] | [[Category: DTDP-4-dehydrorhamnose reductase]] | ||
[[Category: Blankenfeldt, W | [[Category: Blankenfeldt, W]] | ||
[[Category: Giraud, M F | [[Category: Giraud, M F]] | ||
[[Category: Graninger, M | [[Category: Graninger, M]] | ||
[[Category: Kerr, I D | [[Category: Kerr, I D]] | ||
[[Category: Leonard, G A | [[Category: Leonard, G A]] | ||
[[Category: McMiken, H J | [[Category: McMiken, H J]] | ||
[[Category: Messner, P | [[Category: Messner, P]] | ||
[[Category: Naismith, J H | [[Category: Naismith, J H]] | ||
[[Category: Whitfield, C | [[Category: Whitfield, C]] | ||
[[Category: Oxidoreductase]] | [[Category: Oxidoreductase]] | ||
[[Category: Rossman-fold]] | [[Category: Rossman-fold]] | ||
[[Category: Sugar-nucleotide-binding domain]] | [[Category: Sugar-nucleotide-binding domain]] | ||
Revision as of 05:46, 25 December 2014
Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH and dTDP-L-rhamnoseCrystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH and dTDP-L-rhamnose
Structural highlights
Function[RFBD_SALTY] Catalyzes the reduction of dTDP-6-deoxy-L-lyxo-4-hexulose to yield dTDP-L-rhamnose. RmlD uses NADH and NADPH nearly equally well. 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-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) catalyzes the final step in the conversion of dTDP-D-glucose to dTDP-L-rhamnose in an NAD(P)H- and Mg2+-dependent reaction. L-rhamnose biosynthesis is an antibacterial target. The structure of RmlD from Salmonella enterica serovar Typhimurium has been determined, and complexes with NADH, NADPH, and dTDP-L-rhamnose are reported. RmlD differs from other short chain dehydrogenases in that it has a novel dimer interface that contains Mg2+. Enzyme catalysis involves hydride transfer from the nicotinamide ring of the cofactor to the C4'-carbonyl group of the substrate. The substrate is activated through protonation by a conserved tyrosine. NAD(P)H is bound in a solvent-exposed cleft, allowing facile replacement. We suggest a novel role for the conserved serine/threonine residue of the catalytic triad of SDR enzymes. Variation on a theme of SDR. dTDP-6-deoxy-L- lyxo-4-hexulose reductase (RmlD) shows a new Mg2+-dependent dimerization mode.,Blankenfeldt W, Kerr ID, Giraud MF, McMiken HJ, Leonard G, Whitfield C, Messner P, Graninger M, Naismith JH Structure. 2002 Jun;10(6):773-86. PMID:12057193[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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