PDBsum entry 2gcu

Hydrolase

PDB id: 2gcu

Contents

Protein chains

244 a.a. *

Ligands

SO4

EDO ×14

Metals

FE2 ×4

Waters ×1037

* Residue conservation analysis

PDB id:

2gcu

Name:

Hydrolase

Title:

X-ray structure of gene product from arabidopsis thaliana at1g53580

Structure:

Putative hydroxyacylglutathione hydrolase 3. Chain: a, b, c, d. Synonym: glyoxalase ii, glx ii. Engineered: yes

Source:

Arabidopsis thaliana. Thale cress. Organism_taxid: 3702. Gene: at1g53580. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Tetramer (from PQS)

Resolution:

1.48Å R-factor: 0.178 R-free: 0.204

Authors:

J.G.Mccoy,G.E.Wesenberg,G.N.Phillips Jr.,E.Bitto,C.A.Bingman,Center For Eukaryotic Structural Genomics (Cesg)

Key ref:

J.G.McCoy et al. (2006). Structure of an ETHE1-like protein from Arabidopsis thaliana. Acta Crystallogr D Biol Crystallogr, 62, 964-970. PubMed id: 16929096 DOI: 10.1107/S0907444906020592

Date:

14-Mar-06 Release date: 18-Apr-06

Protein chains

Q9C8L4  (ETHE1_ARATH) -  Persulfide dioxygenase ETHE1 homolog, mitochondrial from Arabidopsis thaliana

Seq: 294 a.a.

Struc: 244 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.1.13.11.18 - persulfide dioxygenase.
• Reaction: S-sulfanylglutathione + O2 + H2O = sulfite + glutathione + 2 H⁺

S-sulfanylglutathione + O2 + H2O = sulfite + glutathione (Bound ligand (Het Group name = SO4) matches with 80.00% similarity) + 2 × H(+)

• Cofactor: Fe cation

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

reference

DOI no: 10.1107/S0907444906020592

Acta Crystallogr D Biol Crystallogr 62:964-970 (2006)

PubMed id: 16929096

Structure of an ETHE1-like protein from Arabidopsis thaliana.

J.G.McCoy, C.A.Bingman, E.Bitto, M.M.Holdorf, C.A.Makaroff, G.N.Phillips.

ABSTRACT

The protein product of gene At1g53580 from Arabidopsis thaliana possesses 54% sequence identity to a human enzyme that has been implicated in the rare disorder ethylmalonic encephalopathy. The structure of the At1g53580 protein has been solved to a nominal resolution of 1.48 Angstrom. This structure reveals tertiary structure differences between the ETHE1-like enzyme and glyoxalase II enzymes that are likely to account for differences in reaction chemistry and multimeric state between the two types of enzymes. In addition, the Arabidopsis ETHE1 protein is used as a model to explain the significance of several mutations in the human enzyme that have been observed in patients with ethylmalonic encephalopathy.

Selected figure(s)

Figure 1.
Figure 1 (a) The At1g53580 monomer. Helices are labelled 1-8 and -strands are labelled A-L. Residues known to be involved in human ethylmalonic encephalopathy in human ETHE1 are colored pink. (b) Overlay of the AtETHE1 (cyan) and the GLX2-5 (magenta) monomers. The metal ions from the GLX2-5 structure are colored orange and the iron ion from the AtETHE1 structure is colored gray. Arrows point to changes between the folds of the two enzymes.

Figure 5.
Figure 5 Overlay of the substrate-binding residues from the human glyoxalase II (cyan) with the equivalent residues in the AtETHE1 enzyme (magenta). S-Hydroxybromophenylcarbamoyl glutathione bound to glyoxalase II is colored yellow. Labels correspond to AtETHE1.

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2006, 62, 964-970) copyright 2006.

Figures were selected by an automated process.