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PDBsum entry 1xyb

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Isomerase(intramolecular oxidoreductase) PDB id
1xyb
Jmol
Contents
Protein chains
386 a.a. *
Ligands
GLO ×2
Metals
_MG ×4
Waters ×481
* Residue conservation analysis

References listed in PDB file
Key reference
Title X-Ray crystallographic structures of d-Xylose isomerase-Substrate complexes position the substrate and provide evidence for metal movement during catalysis.
Authors A.Lavie, K.N.Allen, G.A.Petsko, D.Ringe.
Ref. Biochemistry, 1994, 33, 5469-5480. [DOI no: 10.1021/bi00184a016]
PubMed id 8180169
Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a perfect match.
Abstract
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.
Secondary reference #1
Title Isotopic exchange plus substrate and inhibition kinetics of d-Xylose isomerase do not support a proton-Transfer mechanism.
Authors K.N.Allen, A.Lavie, G.K.Farber, A.Glasfeld, G.A.Petsko, D.Ringe.
Ref. Biochemistry, 1994, 33, 1481-1487. [DOI no: 10.1021/bi00172a026]
PubMed id 8312268
Full text Abstract
Secondary reference #2
Title Role of the divalent metal ion in sugar binding, Ring opening, And isomerization by d-Xylose isomerase: replacement of a catalytic metal by an amino acid.
Authors K.N.Allen, A.Lavie, A.Glasfeld, T.N.Tanada, D.P.Gerrity, S.C.Carlson, G.K.Farber, G.A.Petsko, D.Ringe.
Ref. Biochemistry, 1994, 33, 1488-1494. [DOI no: 10.1021/bi00172a027]
PubMed id 7906142
Full text Abstract
PROCHECK
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