PDBsum entry: 1xm8

Hydrolase

PDB id: 1xm8

Contents

Protein chains

254 a.a. *

Ligands

ACY ×2

PEG

Metals

_ZN ×2

_FE ×2

Waters ×547

* Residue conservation analysis

PDB id:

1xm8

Name:

Hydrolase

Title:

X-ray structure of glyoxalase ii from arabidopsis thaliana gene at2g31350

Structure:

Glyoxalase ii. Chain: a, b. Engineered: yes

Source:

Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: at2g31350. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.74Å R-factor: 0.142 R-free: 0.189

Authors:

G.E.Wesenberg,D.W.Smith,G.N.Phillips Jr.,E.Bitto, C.A.Bingman,S.T.M.Allard,Center For Eukaryotic Structural Genomics (Cesg)

Key ref:

G.P.Marasinghe et al. (2005). Structural studies on a mitochondrial glyoxalase II. J Biol Chem, 280, 40668-40675. PubMed id: 16227621 DOI: 10.1074/jbc.M509748200

Date:

01-Oct-04 Release date: 12-Oct-04

Protein chains

Q9SID3  (GLO2N_ARATH) -  Hydroxyacylglutathione hydrolase 2, mitochondrial

Seq: 324 a.a.

Struc: 254 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.1.2.6 - Hydroxyacylglutathione hydrolase.
• Reaction: S-(2-hydroxyacyl)glutathione + H₂O = glutathione + a 2-hydroxy carboxylate

S-(2-hydroxyacyl)glutathione + H(2)O = glutathione + 2-hydroxy carboxylate (Bound ligand (Het Group name = ACY) matches with 66.00% similarity)

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

 Gene Ontology (GO) functional annotation 

• Biochemical function: hydrolase activity (3 terms)

reference

DOI no: 10.1074/jbc.M509748200

J Biol Chem 280:40668-40675 (2005)

PubMed id: 16227621

Structural studies on a mitochondrial glyoxalase II.

G.P.Marasinghe, I.M.Sander, B.Bennett, G.Periyannan, K.W.Yang, C.A.Makaroff, M.W.Crowder.

ABSTRACT

Glyoxalase 2 is a beta-lactamase fold-containing enzyme that appears to be involved with cellular chemical detoxification. Although the cytoplasmic isozyme has been characterized from several organisms, essentially nothing is known about the mitochondrial proteins. As a first step in understanding the structure and function of mitochondrial glyoxalase 2 enzymes, a mitochondrial isozyme (GLX2-5) from Arabidopsis thaliana was cloned, overexpressed, purified, and characterized using metal analyses, EPR and (1)H NMR spectroscopies, and x-ray crystallography. The recombinant enzyme was shown to bind 1.04 +/- 0.15 eq of iron and 1.31 +/- 0.05 eq of Zn(II) and to exhibit k(cat) and K(m) values of 129 +/- 10 s(-1) and 391 +/- 48 microm, respectively, when using S-d-lactoylglutathione as the substrate. EPR spectra revealed that recombinant GLX2-5 contains multiple metal centers, including a predominant Fe(III)Z-n(II) center and an anti-ferromagnetically coupled Fe(III)Fe(II) center. Unlike cytosolic glyoxalase 2 from A. thaliana, GLX2-5 does not appear to specifically bind manganese. (1)H NMR spectra revealed the presence of at least eight paramagnetically shifted resonances that arise from protons in close proximity to a Fe(III)Fe(II) center. Five of these resonances arose from solvent-exchangeable protons, and four of these have been assigned to NH protons on metal-bound histidines. A 1.74-A resolution crystal structure of the enzyme revealed that although GLX2-5 shares a number of structural features with human GLX2, several important differences exist. These data demonstrate that mitochondrial glyoxalase 2 can accommodate a number of different metal centers and that the predominant metal center is Fe(III)Zn(II).

Selected figure(s)

Figure 4.
Ribbon structure of GLX2-5 from A. thaliana. The coordinates have been deposited in the Protein Data Bank (accession number 1XM8). Figure was rendered using Raswin Molecular Graphics, Windows version 2.7.2.1.1.

Figure 5.
Active sites of (left) GLX2-2 from human and (right) GLX2-5 from A. thaliana. Figure was rendered using Raswin Molecular Graphics, Windows version 2.7.2.1.1.

The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2005, 280, 40668-40675) copyright 2005.

Figures were selected by an automated process.