PDBsum entry 3cs2

Hydrolase, metal binding protein

PDB id: 3cs2

Contents

Protein chains

331 a.a. *

Ligands

CAC ×4

Metals

_CO ×8

Waters ×1163

* Residue conservation analysis

PDB id:

3cs2

Name:

Hydrolase, metal binding protein

Title:

Crystal structure of pte g60a mutant

Structure:

Parathion hydrolase. Chain: a, b, k, p. Fragment: residues 34-364. Synonym: phosphotriesterase, pte. Engineered: yes. Mutation: yes

Source:

Brevundimonas diminuta. Pseudomonas diminuta. Organism_taxid: 293. Gene: opd. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.95Å R-factor: 0.170 R-free: 0.224

Authors:

J.Kim,S.C.Almo

Key ref:

J.Kim et al. (2008). Structure of diethyl phosphate bound to the binuclear metal center of phosphotriesterase. Biochemistry, 47, 9497-9504. PubMed id: 18702530

Date:

08-Apr-08 Release date: 17-Feb-09

Protein chains

P0A434  (OPD_BREDI) -  Parathion hydrolase from Brevundimonas diminuta

Seq: 365 a.a.

Struc: 331 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.1.8.1 - aryldialkylphosphatase.
• Reaction: An aryl dialkyl phosphate + H2O = dialkyl phosphate + an aryl alcohol
• Cofactor: Divalent cation

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

Added reference

Biochemistry 47:9497-9504 (2008)

PubMed id: 18702530

Structure of diethyl phosphate bound to the binuclear metal center of phosphotriesterase.

J.Kim, P.C.Tsai, S.L.Chen, F.Himo, S.C.Almo, F.M.Raushel.

ABSTRACT

The bacterial phosphotriesterase (PTE) from Pseudomonas diminuta catalyzes the hydrolysis of organophosphate esters at rates close to the diffusion limit. X-ray diffraction studies have shown that a binuclear metal center is positioned in the active site of PTE and that this complex is responsible for the activation of the nucleophilic water from solvent. In this paper, the three-dimensional structure of PTE was determined in the presence of the hydrolysis product, diethyl phosphate (DEP), and a product analogue, cacodylate. In the structure of the PTE-diethyl phosphate complex, the DEP product is found symmetrically bridging the two divalent cations. The DEP displaces the hydroxide from solvent that normally bridges the two divalent cations in structures determined in the presence or absence of substrate analogues. One of the phosphoryl oxygen atoms in the PTE-DEP complex is 2.0 A from the alpha-metal ion, while the other oxygen is 2.2 A from the beta-metal ion. The two metal ions are separated by a distance of 4.0 A. A similar structure is observed in the presence of cacodylate. Analogous complexes have previously been observed for the product complexes of isoaspartyl dipeptidase, d-aminoacylase, and dihydroorotase from the amidohydrolase superfamily of enzymes. The experimentally determined structure of the PTE-diethyl phosphate product complex is inconsistent with a recent proposal based upon quantum mechanical/molecular mechanical simulations which postulated the formation of an asymmetrical product complex bound exclusively to the beta-metal ion with a metal-metal separation of 5.3 A. This structure is also inconsistent with a chemical mechanism for substrate hydrolysis that utilizes the bridging hydroxide as a base to abstract a proton from a water molecule loosely associated with the alpha-metal ion. Density functional theory (DFT) calculations support a reaction mechanism that utilizes the bridging hydroxide as the direct nucleophile in the hydrolysis of organophosphate esters by PTE.