1xyc
X-RAY CRYSTALLOGRAPHIC STRUCTURES OF D-XYLOSE ISOMERASE-SUBSTRATE COMPLEXES POSITION THE SUBSTRATE AND PROVIDE EVIDENCE FOR METAL MOVEMENT DURING CATALYSIS
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OverviewOverview
The X-ray crystallographic structures of the metal-activated enzyme xylose, isomerase from Streptomyces olivochromogenes with the substrates, D-glucose, 3-O-methyl-D-glucose and in the absence of substrate were, determined to 1.96-, 2.19-, and 1.81-A resolution and refined to R-factors, of 16.6%, 15.9%, and 16.1%, respectively. Xylose isomerase catalyzes the, interconversion between glucose and fructose (xylose and xylulose under, physiological conditions) by utilizing two metal cofactors to promote a, hydride shift; the metals are bridged by a glutamate residue. This puts, xylose isomerase in the small but rapidly growing family of enzymes with a, bridged bimetallic active site, in which both metals are involved in the, chemical transformation. The substrate 3-O-methylglucose was chosen in, order to position the glucose molecule in the observed electron density, unambiguously. Of the two essential magnesium ions per active site, Mg-2, was observed to occupy two alternate positions, separated by 1.8 A, in the, substrate-soaked structures. The deduced movement was not observed in the, structure without substrate present and is attributed to a step following, substrate binding but prior to isomerization. The substrates glucose and, 3-O-methylglucose are observed in their linear extended forms and make, identical interactions with the enzyme by forming ligands to Mg-1 through, O2 and O4 and by forming hydrogen bonds with His53 through O5 and Lys182, through O1. Mg-2 has a water ligand that is interpreted in the crystal, structure in the absence of substrate as a hydroxide ion and in the, presence of substrate as a water molecule. This hydroxide ion may act as a, base to deprotonate the glucose O2 and subsequently protonate the product, fructose O1 concomitant with hydride transfer. Calculations of the, solvent-accessible surface of possible dimers, with and without the, alpha-helical C-terminal domain, suggest that the tetramer is the active, form of this xylose isomerase.
About this StructureAbout this Structure
1XYC is a Single protein structure of sequence from Streptomyces olivochromogenes with 3MF and MG as ligands. Active as Xylose isomerase, with EC number 5.3.1.5 Full crystallographic information is available from OCA.
ReferenceReference
X-ray crystallographic structures of D-xylose isomerase-substrate complexes position the substrate and provide evidence for metal movement during catalysis., Lavie A, Allen KN, Petsko GA, Ringe D, Biochemistry. 1994 May 10;33(18):5469-80. PMID:8180169
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