PDBsum entry: 1p9e

Hydrolase

PDB id: 1p9e

Contents

Protein chains

294 a.a. *

Metals

_NA ×5

_ZN ×3

__K ×4

_CD

Waters ×172

* Residue conservation analysis

PDB id:

1p9e

Name:

Hydrolase

Title:

Crystal structure analysis of methyl parathion hydrolase fro pseudomonas sp wbc-3

Structure:

Methyl parathion hydrolase. Chain: a, b. Ec: 3.1.8.1

Source:

Pseudomonas sp.. Organism_taxid: 165468. Strain: wbc-3

Biol. unit:

Dimer (from PQS)

Resolution:

2.40Å R-factor: 0.218 R-free: 0.259

Authors:

Y.Dong,L.Sun,M.Bartlam,Z.Rao,X.Zhang

Key ref:

Y.J.Dong et al. (2005). Crystal structure of methyl parathion hydrolase from Pseudomonas sp. WBC-3. J Mol Biol, 353, 655-663. PubMed id: 16181636 DOI: 10.1016/j.jmb.2005.08.057

Date:

11-May-03 Release date: 25-May-04

Protein chains

Q841S6  (Q841S6_9PSED) -  Methyl parathion hydrolase

Seq: 331 a.a.

Struc: 294 a.a.

 Gene Ontology (GO) functional annotation 

• Biochemical function: hydrolase activity (2 terms)

DOI no: 10.1016/j.jmb.2005.08.057

J Mol Biol 353:655-663 (2005)

PubMed id: 16181636

Crystal structure of methyl parathion hydrolase from Pseudomonas sp. WBC-3.

Y.J.Dong, M.Bartlam, L.Sun, Y.F.Zhou, Z.P.Zhang, C.G.Zhang, Z.Rao, X.E.Zhang.

ABSTRACT

Methyl parathion hydrolase (MPH, E.C.3.1.8.1), isolated from the soil-dwelling bacterium Pseudomonas sp. WBC-3, is a Zn(II)-containing enzyme that catalyzes the degradation of the organophosphate pesticide methyl parathion. We have determined the structure of MPH from Pseudomonas sp. WBC-3 to 2.4 angstroms resolution. The enzyme is dimeric and each subunit contains a mixed hybrid binuclear zinc center, in which one of the zinc ions is replaced by cadmium. In both subunits, the more solvent-exposed beta-metal ion is substituted for Cd2+ due to high cadmium concentration in the crystallization condition. Both ions are surrounded by ligands in an octahedral arrangement. The ions are separated by 3.5 angstroms and are coordinated by the amino acid residues His147, His149, Asp151, His152, His234 and His302 and a water molecule. Asp255 and a water molecule serve to bridge the zinc ions together. MPH is homologous with other metallo-beta-lactamases but does not show any similarity to phosphotriesterase that can also catalyze the degradation of methyl parathion with lower rate, despite the lack of sequence homology. Trp179, Phe196 and Phe119 form an aromatic cluster at the entrance of the catalytic center. Replacement of these three amino acids by alanine resulted in a significant increase of K(m) and loss of catalytic activity, indicating that the aromatic cluster has an important role to facilitate affinity of enzyme to the methyl parathion substrates.

Selected figure(s)

Figure 1.
Figure 1. (a) The chemical structures of parathion and methyl parathion, and the reaction for the hydrolysis of methyl parathion. (b) A cartoon representation of the monomer structure of MPH. The structure is colored from blue at the N terminus to red at the C terminus. The two metal ions are shown as silver (Zn) and gold (Cd) spheres. (c) A cartoon representation of the MPH dimer. Protomer A is shown in red and protomer B is shown in blue. The metal ions are shown as silver (Zn) and gold (Cd) spheres. (d) A molecular surface view of the MPH dimer. Coloring is as in (c).

Figure 3.
Figure 3. Superposition of metal centers. Structural homologs of MPH were identified using DALI (www.ebi.ac.uk/dali/). The color key is as follows: MPH, yellow; ROO (1E5D), magenta; metallo-b-lactamase (1A7T), green; metallo-b-lactamase (1SML), salmon; human glyoxalase II (1QH5), cyan.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 353, 655-663) copyright 2005.

Figures were selected by an automated process.