PDBsum entry 3kcl

Isomerase

PDB id

3kcl

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Contents

			Protein chain

					388 a.a. *

			Ligands

					GLC


					DOD ×199

			Metals

					_CD ×2

* Residue conservation analysis

PDB id:

3kcl

Links

Name:

Isomerase

Title:

Room temperature neutron structure of d-xylose isomerase in complex with two cd2+ cations and d12-d-alpha-glucose in the ring form (refined jointly with x-ray structure 3kbm)

Structure:

Xylose isomerase. Chain: a. Engineered: yes

Source:

Streptomyces rubiginosus. Organism_taxid: 1929. Gene: xyla

Resolution:

2.00Å

R-factor:

0.188

R-free:

0.211

Authors:

A.Y.Kovalevsky,P.Langan

Key ref:

A.Y.Kovalevsky et al. (2010). Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study. Structure, 18, 688-699. PubMed id: 20541506

Date:

21-Oct-09

Release date:

16-Jun-10

PROCHECK

	Headers

	References

Protein chain

P24300 (XYLA_STRRU) - Xylose isomerase from Streptomyces rubiginosus

Seq: Struc:					388 a.a. 388 a.a.

Key:

PfamA domain

Secondary structure

CATH domain



		Enzyme reactions

Enzyme class:

E.C.5.3.1.5 - xylose isomerase.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

alpha-D-xylose = alpha-D-xylulofuranose

alpha-D-xylose
Bound ligand (Het Group name = GLC)
matches with 41.67% similarity

alpha-D-xylulofuranose

Cofactor:

Mg(2+)

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

Key reference

	Structure 18:688-699 (2010)
PubMed id: 20541506

Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study.
A.Y.Kovalevsky, L.Hanson, S.Z.Fisher, M.Mustyakimov, S.A.Mason, V.T.Forsyth, M.P.Blakeley, D.A.Keen, T.Wagner, H.L.Carrell, A.K.Katz, J.P.Glusker, P.Langan.

ABSTRACT

Conversion of aldo to keto sugars by the metalloenzyme D-xylose isomerase (XI) is a multistep reaction that involves hydrogen transfer. We have determined the structure of this enzyme by neutron diffraction in order to locate H atoms (or their isotope D). Two studies are presented, one of XI containing cadmium and cyclic D-glucose (before sugar ring opening has occurred), and the other containing nickel and linear D-glucose (after ring opening has occurred but before isomerization). Previously we reported the neutron structures of ligand-free enzyme and enzyme with bound product. The data show that His54 is doubly protonated on the ring N in all four structures. Lys289 is neutral before ring opening and gains a proton after this; the catalytic metal-bound water is deprotonated to hydroxyl during isomerization and O5 is deprotonated. These results lead to new suggestions as to how changes might take place over the course of the reaction.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21481775

T.D.Fenn, M.J.Schnieders, M.Mustyakimov, C.Wu, P.Langan, V.S.Pande, and A.T.Brunger (2011).
Reintroducing electrostatics into macromolecular crystallographic refinement: application to neutron crystallography and DNA hydration.

Structure, 19, 523-533.

PDB code:

3qba

20541500

B.C.Bennett, and M.Yeager (2010).
The lighter side of a sweet reaction.

Structure, 18, 657-659.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.