1kc1: Difference between revisions

Revision as of 14:32, 21 February 2008

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

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

1KC1 is a Single protein structure of sequence from Salmonella typhimurium with , and as ligands. Active as dTDP-4-dehydrorhamnose reductase, with EC number 1.1.1.133 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

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OCA

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-[[Image:1kc1.jpg|left|200px]]<br /><applet load="1kc1" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1kc1.jpg|left|200px]]<br /><applet load="1kc1" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1kc1, resolution 2.60&Aring;" />
 '''Crystal structure of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD) in complex with NADPH'''<br />
 ==Overview==
-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.
+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 Structure==
-KC1 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_typhimurium Salmonella typhimurium] with MG, SO4 and NDP as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1KC1 OCA].
+KC1 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Salmonella_typhimurium Salmonella typhimurium] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=NDP:'>NDP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KC1 OCA].
 ==Reference==
@@ Line 15: / Line 15: @@
 [[Category: dTDP-4-dehydrorhamnose reductase]]
 [[Category: Blankenfeldt, W.]]
-[[Category: Giraud, M.F.]]
+[[Category: Giraud, M F.]]
 [[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: Naismith, J.H.]]
+[[Category: Naismith, J H.]]
 [[Category: Whitfield, C.]]
 [[Category: MG]]
@@ Line 29: / Line 29: @@
 [[Category: sugar-nucleotide-binding domain]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 19:02:37 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:32:24 2008''