1KC3

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

Summary for 1KC3

• Entry DOI: 10.2210/pdb1kc3/pdb
• Related: 1KBZ 1KC0 1KC1
• Descriptor: dTDP-glucose oxidoreductase, MAGNESIUM ION, NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE, ... (5 entities in total)
• Functional Keywords: rossman-fold, sugar-nucleotide-binding domain, oxidoreductase
• Biological source: Salmonella typhimurium
• Total number of polymer chains: 1
• Total formula weight: 33908.00

Authors

Blankenfeldt, W.,Kerr, I.D.,Giraud, M.F.,McMiken, H.J.,Leonard, G.A.,Whitfield, C.,Messner, P.,Graninger, M.,Naismith, J.H. (deposition date: 2001-11-07, release date: 2002-06-28, Last modification date: 2024-02-07)

Primary citation

Blankenfeldt, W.,Kerr, I.D.,Giraud, M.F.,McMiken, H.J.,Leonard, G.,Whitfield, C.,Messner, P.,Graninger, M.,Naismith, J.H.
Variation on a theme of SDR. dTDP-6-deoxy-L- lyxo-4-hexulose reductase (RmlD) shows a new Mg2+-dependent dimerization mode.
Structure, 10:773-786, 2002

PubMed Abstract: 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.

PubMed: 12057193
DOI: 10.1016/S0969-2126(02)00770-0

Experimental method

X-RAY DIFFRACTION (2.7 Å)