PDBsum entry 3u3h

Isomerase

PDB id: 3u3h

Contents

Protein chain

386 a.a.

Ligands

03W

FMT

MRD

Metals

_MG ×2

Waters ×524

PDB id:

3u3h

Name:

Isomerase

Title:

X-ray crystallographic analysis of d-xylose isomerase-catalyzed isomerization of (r)-glyceraldehyde

Structure:

Xylose isomerase. Chain: a. Ec: 5.3.1.5

Source:

Streptomyces rubiginosus. Organism_taxid: 1929

Resolution:

0.97Å R-factor: 0.116 R-free: 0.125

Authors:

K.N.Allen,N.R.Silvaggi,M.M.Toteva,J.P.Richard

Key ref:

M.M.Toteva et al. (2011). Binding energy and catalysis by D-xylose isomerase: kinetic, product, and X-ray crystallographic analysis of enzyme-catalyzed isomerization of (R)-glyceraldehyde. Biochemistry, 50, 10170-10181. PubMed id: 21995300

Date:

05-Oct-11 Release date: 26-Oct-11

Protein chain

P24300  (XYLA_STRRU) -  Xylose isomerase from Streptomyces rubiginosus

Seq: 388 a.a.

Struc: 386 a.a.

Enzyme reactions

• Enzyme class: E.C.5.3.1.5 - xylose isomerase.
• Reaction: alpha-D-xylose = alpha-D-xylulofuranose

alpha-D-xylose (Bound ligand (Het Group name = 03W) matches with 70.00% similarity) = alpha-D-xylulofuranose

• Cofactor: Mg(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

Biochemistry 50:10170-10181 (2011)

PubMed id: 21995300

Binding energy and catalysis by D-xylose isomerase: kinetic, product, and X-ray crystallographic analysis of enzyme-catalyzed isomerization of (R)-glyceraldehyde.

M.M.Toteva, N.R.Silvaggi, K.N.Allen, J.P.Richard.

ABSTRACT

D-Xylose isomerase (XI) and triosephosphate isomerase (TIM) catalyze the aldose-ketose isomerization reactions of D-xylose and d-glyceraldehyde 3-phosphate (DGAP), respectively. D-Glyceraldehyde (DGA) is the triose fragment common to the substrates for XI and TIM. The XI-catalyzed isomerization of DGA to give dihydroxyacetone (DHA) in D(2)O was monitored by (1)H nuclear magnetic resonance spectroscopy, and a k(cat)/K(m) of 0.034 M(-1) s(-1) was determined for this isomerization at pD 7.0. This is similar to the k(cat)/K(m) of 0.017 M(-1) s(-1) for the TIM-catalyzed carbon deprotonation reaction of DGA in D(2)O at pD 7.0 [Amyes, T. L., O'Donoghue, A. C., and Richard, J. P. (2001) J. Am. Chem. Soc. 123, 11325-11326]. The much larger activation barrier for XI-catalyzed isomerization of D-xylose (k(cat)/K(m) = 490 M(-1) s(-1)) versus that for the TIM-catalyzed isomerization of DGAP (k(cat)/K(m) = 9.6 × 10(6) M(-1) s(-1)) is due to (i) the barrier to conversion of cyclic d-xylose to the reactive linear sugar (5.4 kcal/mol) being larger than that for conversion of DGAP hydrate to the free aldehyde (1.7 kcal/mol) and (ii) the intrinsic binding energy [Jencks, W. P. (1975) Adv. Enzymol. Relat. Areas Mol. Biol. 43, 219-410] of the terminal ethylene glycol fragment of D-xylose (9.3 kcal/mol) being smaller than that of the phosphodianion group of DGAP (~12 kcal/mol). The XI-catalyzed isomerization of DGA in D(2)O at pD 7.0 gives a 90% yield of [1-(1)H]DHA and a 10% yield of [1-(2)H]DHA, the product of isomerization with incorporation of deuterium from solvent D(2)O. By comparison, the transfer of (3)H from the labeled hexose substrate to solvent is observed only once in every 10(9) turnovers for the XI-catalyzed isomerization of [2-(3)H]glucose in H(2)O [Allen, K. N., Lavie, A., Farber, G. K., Glasfeld, A., Petsko, G. A., and Ringe, D. (1994) Biochemistry 33, 1481-1487]. We propose that truncation of the terminal ethylene glycol fragment of d-xylose to give DGA results in a large decrease in the rate of XI-catalyzed isomerization with hydride transfer compared with that for proton transfer. An ultra-high-resolution (0.97 Å) X-ray crystal structure was determined for the complex obtained by soaking crystals of XI with 50 mM DGA. The triose binds to XI as the unreactive hydrate, but ligand binding induces metal cofactor movement and conformational changes in active site residues similar to those observed for XI·sugar complexes.