PDBsum entry 1xii

Isomerase(intramolecular oxidoreductase)

PDB id: 1xii

Contents

Protein chain

385 a.a. *

Ligands

XUL

Metals

_MN ×2

Waters ×300

* Residue conservation analysis

PDB id:

1xii

Name:

Isomerase(intramolecular oxidoreductase)

Title:

Modes of binding substrates and their analogues to the enzyme d-xylose isomerase

Structure:

D-xylose isomerase. Chain: a. Engineered: yes

Source:

Streptomyces rubiginosus. Organism_taxid: 1929

Biol. unit:

Tetramer (from PQS)

Resolution:

1.70Å R-factor: 0.147

Authors:

H.L.Carrell,J.P.Glusker

Key ref:

H.L.Carrell et al. (1994). Modes of binding substrates and their analogues to the enzyme D-xylose isomerase. Acta Crystallogr D Biol Crystallogr, 50, 113-123. PubMed id: 15299449 DOI: 10.1107/S0907444993009345

Date:

07-Mar-94 Release date: 22-Jun-94

Protein chain

P24300  (XYLA_STRRU) -  Xylose isomerase from Streptomyces rubiginosus

Seq: 388 a.a.

Struc: 385 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

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 = XUL) corresponds exactly) = alpha-D-xylulofuranose

• Cofactor: Mg(2+)

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

Key reference

DOI no: 10.1107/S0907444993009345

Acta Crystallogr D Biol Crystallogr 50:113-123 (1994)

PubMed id: 15299449

Modes of binding substrates and their analogues to the enzyme D-xylose isomerase.

H.L.Carrell, H.Hoier, J.P.Glusker.

ABSTRACT

Studies of binding of substrates and inhibitors of the enzyme D-xylose isomerase show, from X-ray diffraction data at 1.6-1.9 A resolution, that there are a variety of binding modes. These vary in the manner in which the substrate or its analogue extend, on binding, across the carboxy end of the (betaalpha)(8)-barrel structure. These binding sites are His54 and the metal ion (magnesium or manganese) that is held in place by Glul81, Asp245, Glu217 and Asp287. Possible catalytic groups have been identified in proposed mechanisms and their role in the binding of ligands is illustrated.

Selected figure(s)

Figure 4.
Fig. 4. Binding of D-glucose. (a) Ball-and-stick view and (b) identification of some binding groups.

Figure 10.
Fig. 10. Binding of D-alkylation product (Carrell e/al., 1989). (a) Ball-and-stick view and (b) identification of some binding groups.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1994, 50, 113-123) copyright 1994.

Figures were selected by an automated process.