X-ray analysis of D-xylose isomerase: Native enzyme in complex with substrate and with a mechanism-designed inactivator

Journal Article · Thu Jun 01 04:00:00 UTC 1989 · Proceedings of the National Academy of Sciences of the United States of America; (USA)

DOI:https://doi.org/10.1073/pnas.86.12.4440· OSTI ID:5350768

Carrell, H L; Glusker, J P; Burger, V; Manfre, F; Tritsch, D; Biellmann, J F ^[1]

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1. Fox Chase Cancer Center, Philadelphia, PA (USA)

The structures of crystalling D-xylose isomerase from Streptomyces rubiginosus and of its complexes with substrate and with an active-site-directed inhibitor have been determined by x-ray diffraction techniques and refined to 1.9-{angstrom} resolution. This study identifies the active site, as well as two metal-binding sites. The metal ions are important in maintaining the structure of the active-site region and one of them binds C{sup 3}-O and C{sup 5}-O of the substrate forming a six-membered ring. This study has revealed a very close contact between histidine and C{sup 1} of a substrate, suggesting that this is the active-site base that abstracts a proton from substrate. The mechanism-based inhibitor is a substrate analog and is turned over by the enzyme to give a product that alkylates this same histidine, reinforcing the authors' interpretation. The changes in structure of the native enzyme, the enzyme with bound substrate, and the alkylated enzyme indicate that the mechanism involves an open-chain conformation of substrate and that the intermediate in the isomerization reaction is probably a cis-ene diol because the active-site histidine is correctly placed to abstract a proton from C{sup 1} or C{sup 2} of the substrate. A water molecule binds to C{sup 1}O and C{sup 2}O of the substrate and so may act as a proton donor or acceptor in the enolization of a ring-opened substrate.

• OSTI ID: 5350768
• Journal Information: Proceedings of the National Academy of Sciences of the United States of America; (USA), Journal Name: Proceedings of the National Academy of Sciences of the United States of America; (USA) Vol. 86:12; ISSN 0027-8424; ISSN PNASA
• Country of Publication: United States
• Language: English

Related Subjects

550602* -- Medicine-- External Radiation in Diagnostics-- (1980-)
62 RADIOLOGY AND NUCLEAR MEDICINE
ALDEHYDES
BACTERIA
CARBOHYDRATES
COHERENT SCATTERING
DIFFRACTION
ENZYME INHIBITORS
ENZYMES
ISOMERASES
MICROORGANISMS
MONOSACCHARIDES
ORGANIC COMPOUNDS
PENTOSES
SACCHARIDES
SCATTERING
STEREOCHEMISTRY
STREPTOMYCES
SUBSTRATES
X-RAY DIFFRACTION
XYLOSE