1oc2

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spinqualitylabelsall models 1oc2, resolution 1.50Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

THE STRUCTURE OF NADH IN THE DTDP-D-GLUCOSE DEHYDRATASE (RMLB) ENZYME

Overview

The structure of Streptococcus suis serotype type 2 dTDP-d-glucose, 4,6-dehydratase (RmlB) has been determined to 1.5 A resolution with its, nicotinamide coenzyme and substrate analogue dTDP-xylose bound in an, abortive complex. During enzyme turnover, NAD(+) abstracts a hydride from, the C4' atom of dTDP-glucose-forming NADH. After elimination of water, hydride is then transferred back to the C6' atom of, dTDP-4-keto-5,6-glucosene-regenerating NAD(+). Single-crystal, spectroscopic studies unambiguously show that the coenzyme has been, trapped as NADH in the crystal. Electron density clearly demonstrates that, in contrast to native structures of RmlB where a flat nicotinamide ring is, observed, the dihydropyridine ring of the reduced cofactor in this complex, is found as a boat. The si face, from which the pro-S hydride is, transferred, has a concave surface. Ab initio electronic structure, calculations demonstrate that the presence of an internal hydrogen bond, between the amide NH on the nicotinamide ring and one of the oxygen atoms, on a phosphate group, stabilizes this distorted conformation., Additionally, calculations show that the hydride donor ability of NADH is, influenced by the degree of bending in the ring and may be influenced by, an active-site tyrosine residue (Tyr 161). These results demonstrate the, ability of dehydratase enzymes to fine-tune the redox potential of NADH, through conformational changes in the nicotinamide ring.

About this Structure

1OC2 is a Single protein structure of sequence from Streptococcus suis with SO4, TDX and NAD as ligands. Active as dTDP-glucose 4,6-dehydratase, with EC number 4.2.1.46 Known structural/functional Site: . Full crystallographic information is available from OCA.

Reference

The structure of NADH in the enzyme dTDP-d-glucose dehydratase (RmlB)., Beis K, Allard ST, Hegeman AD, Murshudov G, Philp D, Naismith JH, J Am Chem Soc. 2003 Oct 1;125(39):11872-8. PMID:14505409

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