A metal‐mediated hydride shift mechanism for xylose isomerase based on the 1.6 Å Streptomycs rubiginosus structure with xylitol and D‐xylose

Proteins: Structure, Function and Bioinformatics - Tập 9 Số 3 - Trang 153-173 - 1991
Marc Whitlow1, Andrew Howard1, B.C. Finzel1, T.L. Poulos1, Evon Winborne1, Gary L. Gilliland1
1Department of Protein Engineering, Genex Corporation, 16020 Industrial Dr., Gaithersburg, Maryland 20877

Tóm tắt

AbstractThe crystal structure of recombinant Streptomyces rubiginous D‐xylose isomerase (D‐xylose keto‐isomerase, EC 5.3.1.5) solved by the multiple isomorphous replacement technique has been refined to R = 0.16 at 1.64 Å resolution. As observed in an earlier study at 4.0 Å (Carrell et al., J. Biol. Chem. 259: 3230–3236, 1984), xylose isomerase is a tetramer composed of four identical subunits. The monomer consists of an eight‐stranded parallel β‐barrel surrounded by eight helices with an extended C‐terminal tail that provides extensive contacts with a neighboring monomer. The active site pocket is defined by an opening in the barrel whose entrance is lined with hydrophobic residues while the bottom of the pocket consists mainly of glutamate, aspartate, and histidine residues coordinated to two manganese ions.The structures of the enzyme in the presence of MnCl2, the inhibitor xylitol, and the substrate D‐xylose in the presence and absence of MnCl2 have also been refined to R = 0.14 at 1.60 Å, R = 0.15 at 1.71 Å, R = 0.15 at 1.60 Å, and R = 0.14 at 1.60 Å, respectively. Both the ring oxygen of the cyclic α‐D‐xylose and its C1 hydroxyl are within hydrogen bonding distance of NE2 of His‐54 in the structure crystallized in the presence of D‐xylose. Both the inhibitor, xylitol, and the extended form of the substrate, D‐xylose, bind such that the C2 and C4 OH groups interact with one of the two divalent cations found in the active site and the C1 OH with the other cation. The remainder of the OH groups hydrogen bond with neighboring amino acid side chains.A detailed mechanism for D‐xylose isomerase is proposed. Upon binding of cyclic α‐D‐xylose to xylose isomerase, His‐54 acts as the catalytic base in a ring opening reaction. The ring opening step is followed by binding of D‐xylose, in volving two divalent cations, in an extended conformation. The isomerization of D‐xylose to D‐xylulose involves a metal‐mediated 1,2‐hydride shift. The final step in the mechanism is a ring closure to produce α‐D‐xylulose. The ring closing is the reverse of the ring opening step.This mechanism accounts for the majority of xylose iomerase's biochemical properties, in cluding (1) the lack of solvent exchange between the 2‐position of D‐xylose and the 1‐pro‐R position of D‐xylulose, (2) the chemical modification of histidine and lysine, (3) the pH vs. activity profile, and (4) the requirement for two divalent cations in the mechanism.

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Tài liệu tham khảo

10.1021/ja01109a516

10.1016/0003-9861(54)90313-6

Bucke C., 1977, Topics in Enzyme and Fermentation Biotechnology, 147

10.1021/cen-v064n037.p011

Sfiligoj E., 1989, HFCS: Riding high as per caps climb

Hogue‐Angeletti R. A., 1975, Subunit structure and amino acid composition of xylose isomerase from Streptomyces albus, J. Biol. Chem., 250, 7814, 10.1016/S0021-9258(19)40888-0

Lobry de Bruyn C. A., 1895, Action des alcalis sur les sucres, II Rec, Trav. Chim., 14, 195

Lobry de Bruyn C. A., 1897, Action des alcalis sur les sucres. IV & VI Rec, Trav. Chim., 16, 241

10.1016/S0096-5332(08)60352-5

10.1002/cber.19000330361

Topper Y. J., 1951, The alkali‐catalyzed conversion of glucose into fructose and mannose, J. Biol. Chem., 189, 191, 10.1016/S0021-9258(18)56109-3

10.1139/v71-235

10.1021/ja00834a031

10.1016/0003-9861(77)90228-4

10.1016/0005-2744(69)90405-7

10.3891/acta.chem.scand.37b-0101

10.1021/bi00782a019

10.1002/recl.19841031206

10.1016/0141-0229(86)90069-4

10.1002/star.19840360107

10.1271/bbb1961.34.1805

10.1271/bbb1961.35.997

10.1016/0141-0229(88)90064-6

10.1042/bj2500285

10.1073/pnas.86.12.4440

10.1073/pnas.87.4.1362

Carrell H. L., 1984, X‐ray crystal structure of D‐xylose isomerase at 4‐Å resolution, J. Biol. Chem., 259, 3230, 10.1016/S0021-9258(17)43285-6

Wong H. C. Ting Y. Myambo K. Watt K. W. Toy P. L. Drummond R. J.Xylose isomerse gene fromStreptomyces rubiginosus: Molecular cloning sequencing and expression of the structural gene.Nucleic Acids Res. 1989 submitted.

10.1016/S0076-6879(84)04104-5

10.1107/S0021889887086436

Hull S. R., 1980, XTAL: New concepts in program system design, Acta Crystallogr., 36, 379

10.1107/S0021889878013308

10.1107/S0567740870002078

Hendrickson W. A. Wyckoff H. W. Hirs C. H. W. Timasheff S. N. eds. Stereochemically restrained refinement of macromolecular structures.Methods Enzymol.115:252–270 1985.

10.1107/S0021889887087144

10.1107/S0567739478001618

Agarwal R. C.New results on fast Fourier least‐squares refinement technique. In: “Refinement of Protein Structures Proceedings of the Daresbury Conference.” Daresbury Lab. UK 1980:24–28.

10.1016/S0022-2836(77)80200-3

Schray K. J., 1972, Kinetic and magnetic resonance studies of the mechanism of D‐xylose isomerase, J. Biol. Chem., 247, 2031, 10.1016/S0021-9258(19)45486-0

10.1016/0022-2836(82)90536-8

10.1038/255609a0

10.1016/0022-2836(79)90416-9

10.1016/0022-2836(89)90092-2

10.1002/prot.340050208

10.1093/protein/1.6.459

10.1093/protein/1.6.467

10.1016/0022-2836(82)90513-7

Young J. M., 1975, Proton magnetic relaxatin studies of the interaction of D‐xylose and xylitol with D‐xylose isomerase, J. Biol. Chem., 250, 9021, 10.1016/S0021-9258(19)40688-1

10.1146/annurev.bi.55.070186.001443

10.1038/329561a0

Whitlow M. Howard A. J.1.6 Å Structures of xylose isomerase fromStreptomyces rubiginosuswith xylitol and xylose and their mechanistic implications. Transact.Am. Crystallogr. Assoc.25:in press 1989.

10.1016/0022-2836(90)90316-E

10.1021/bi00444a022

10.1021/ja01122a065

Blackburn S., 1976, Enzyme Structure and Function, 62

10.1021/bi00435a001

10.1073/pnas.76.6.2551

10.1021/bi00379a014

10.1021/bi00437a026

10.1098/rstb.1981.0069

10.1073/pnas.85.1.112

10.1002/prot.340040303

10.1016/0167-4838(86)90039-7

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Proteins: Structure, Function and Bioinformatics

Tập 9 Số 3

153-173

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