4dvo

Room-temperature joint X-ray/neutron structure of D-xylose isomerase in complex with 2Ni2+ and per-deuterated D-sorbitol at pH 5.9

spinqualitylabelsall models 4dvo, resolution 2.00Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 4dvo is a 1 chain structure with sequence from Streptomyces rubiginosus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: DOD, NI, SOR Related: 4duo Activity: Xylose isomerase, with EC number 5.3.1.5 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [XYLA_STRRU] Involved in D-xylose catabolism. Publication Abstract from PubMed D-Xylose isomerase (XI) converts the aldo-sugars xylose and glucose to their keto analogs xylulose and fructose, but is strongly inhibited by the polyols xylitol and sorbitol, especially at acidic pH. In order to understand the atomic details of polyol binding to the XI active site, a 2.0 A resolution room-temperature joint X-ray/neutron structure of XI in complex with Ni(2+) cofactors and sorbitol inhibitor at pH 5.9 and a room-temperature X-ray structure of XI containing Mg(2+) ions and xylitol at the physiological pH of 7.7 were obtained. The protonation of oxygen O5 of the inhibitor, which was found to be deprotonated and negatively charged in previous structures of XI complexed with linear glucose and xylulose, was directly observed. The Ni(2+) ions occupying the catalytic metal site (M2) were found at two locations, while Mg(2+) in M2 is very mobile and has a high B factor. Under acidic conditions sorbitol gains a water-mediated interaction that connects its O1 hydroxyl to Asp257. This contact is not found in structures at basic pH. The new interaction that is formed may improve the binding of the inhibitor, providing an explanation for the increased affinity of the polyols for XI at low pH. Inhibition of D-xylose isomerase by polyols: atomic details by joint X-ray/neutron crystallography.,Kovalevsky A, Hanson BL, Mason SA, Forsyth VT, Fisher Z, Mustyakimov M, Blakeley MP, Keen DA, Langan P Acta Crystallogr D Biol Crystallogr. 2012 Sep;68(Pt 9):1201-6. Epub 2012 Aug 18. PMID:22948921 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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