1kc3: Difference between revisions

Revision as of 22:33, 2 May 2008

Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH and dTDP-L-rhamnose

OverviewOverview

dTDP-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.

About this StructureAbout this Structure

1KC3 is a Single protein structure of sequence from Salmonella typhimurium. Full crystallographic information is available from OCA.

ReferenceReference

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 Page seeded by OCA on Fri May 2 22:33:40 2008

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OCA

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 [[Image:1kc3.jpg|left|200px]]
- {{Structure
+<!--
-|PDB= 1kc3 |SIZE=350|CAPTION= <scene name='initialview01'>1kc3</scene>, resolution 2.70&Aring;
+The line below this paragraph, containing "STRUCTURE_1kc3", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <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&#39;-DEOXY-THYMIDINE-BETA-L-RHAMNOSE'>TRH</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|ACTIVITY= <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>
+or leave the SCENE parameter empty for the default display.
-|GENE= rfbA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=602 Salmonella typhimurium])
+-->
-|DOMAIN=
+{{STRUCTURE_1kc3|  PDB=1kc3  |  SCENE=  }}
-|RELATEDENTRY=[[1kbz|1KBZ]], [[1kc0|1KC0]], [[1kc1|1KC1]]
-|RESOURCES=<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.ebi.ac.uk/pdbsum/1kc3 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1kc3 RCSB]</span>
-}}
 '''Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH and dTDP-L-rhamnose'''
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 [[Category: Salmonella typhimurium]]
 [[Category: Single protein]]
-[[Category: dTDP-4-dehydrorhamnose reductase]]
+[[Category: DTDP-4-dehydrorhamnose reductase]]
 [[Category: Blankenfeldt, W.]]
 [[Category: Giraud, M F.]]
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 [[Category: Naismith, J H.]]
 [[Category: Whitfield, C.]]
-[[Category: rossman-fold]]
+[[Category: Rossman-fold]]
-[[Category: sugar-nucleotide-binding domain]]
+[[Category: Sugar-nucleotide-binding domain]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 22:33:40 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:46:23 2008''