PDBsum entry 1k8c

Oxidoreductase

PDB id: 1k8c

Contents

Protein chains

317 a.a. *

Ligands

NAP ×4

Waters ×734

* Residue conservation analysis

PDB id:

1k8c

Name:

Oxidoreductase

Title:

Crystal structure of dimeric xylose reductase in complex with NADP(h)

Structure:

Xylose reductase. Chain: a, b, c, d. Synonym: NAD(p)h-dependent xylose reductase. Xr. Engineered: yes

Source:

Candida tenuis. Organism_taxid: 45596. Gene: xylr. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biol. unit:

Dimer (from PQS)

Resolution:

2.10Å R-factor: 0.213 R-free: 0.243

Authors:

K.L.Kavanagh,M.Klimacek,B.Nidetzky,D.K.Wilson

Key ref:

K.L.Kavanagh et al. (2002). The structure of apo and holo forms of xylose reductase, a dimeric aldo-keto reductase from Candida tenuis. Biochemistry, 41, 8785-8795. PubMed id: 12102621 DOI: 10.1021/bi025786n

Date:

23-Oct-01 Release date: 05-Jul-02

Protein chains

O74237  (XYL1_CANTE) -  NAD(P)H-dependent D-xylose reductase from Candida tenuis

Seq: 322 a.a.

Struc: 317 a.a.

Enzyme reactions

• Enzyme class: E.C.1.1.1.307 - D-xylose reductase [NAD(P)H].
• Reaction:
  1. xylitol + NAD⁺ = D-xylose + NADH + H⁺
  2. xylitol + NADP⁺ = D-xylose + NADPH + H⁺

xylitol (Bound ligand (Het Group name = NAP) matches with 91.67% similarity) + NAD(+) = D-xylose + NADH + H(+)

xylitol (Bound ligand (Het Group name = NAP) corresponds exactly) + NADP(+) = D-xylose + NADPH + H(+)

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

reference

DOI no: 10.1021/bi025786n

Biochemistry 41:8785-8795 (2002)

PubMed id: 12102621

The structure of apo and holo forms of xylose reductase, a dimeric aldo-keto reductase from Candida tenuis.

K.L.Kavanagh, M.Klimacek, B.Nidetzky, D.K.Wilson.

ABSTRACT

Xylose reductase is a homodimeric oxidoreductase dependent on NADPH or NADH and belongs to the largely monomeric aldo-keto reductase superfamily of proteins. It catalyzes the first step in the assimilation of xylose, an aldose found to be a major constituent monosaccharide of renewable plant hemicellulosic material, into yeast metabolic pathways. It does this by reducing open chain xylose to xylitol, which is reoxidized to xylulose by xylitol dehydrogenase and metabolically integrated via the pentose phosphate pathway. No structure has yet been determined for a xylose reductase, a dimeric aldo-keto reductase or a family 2 aldo-keto reductase. The structures of the Candida tenuis xylose reductase apo- and holoenzyme, which crystallize in spacegroup C2 with different unit cells, have been determined to 2.2 A resolution and an R-factor of 17.9 and 20.8%, respectively. Residues responsible for mediating the novel dimeric interface include Asp-178, Arg-181, Lys-202, Phe-206, Trp-313, and Pro-319. Alignments with other superfamily members indicate that these interactions are conserved in other dimeric xylose reductases but not throughout the remainder of the oligomeric aldo-keto reductases, predicting alternate modes of oligomerization for other families. An arrangement of side chains in a catalytic triad shows that Tyr-52 has a conserved function as a general acid. The loop that folds over the NAD(P)H cosubstrate is disordered in the apo form but becomes ordered upon cosubstrate binding. A slow conformational isomerization of this loop probably accounts for the observed rate-limiting step involving release of cosubstrate. Xylose binding (K(m) = 87 mM) is mediated by interactions with a binding pocket that is more polar than a typical aldo-keto reductase. Modeling of xylose into the active site of the holoenzyme using ordered waters as a guide for sugar hydroxyls suggests a convincing mode of substrate binding.