3CAK

X-ray structure of WT PTE with ethyl phosphate

Summary for 3CAK

• Entry DOI: 10.2210/pdb3cak/pdb
• Descriptor: Parathion hydrolase, COBALT (II) ION, 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL, ... (6 entities in total)
• Functional Keywords: protein-product complex, hydrolase, membrane, metal-binding, plasmid
• Biological source: Brevundimonas diminuta
• Cellular location: Cell membrane; Peripheral membrane protein: P0A434
• Total number of polymer chains: 2
• Total formula weight: 72854.28

Authors

Kim, J.,Tsai, P.-C.,Almo, S.C.,Raushel, F.M. (deposition date: 2008-02-20, release date: 2008-10-21, Last modification date: 2023-11-15)

Primary citation

Kim, J.,Tsai, P.C.,Chen, S.L.,Himo, F.,Almo, S.C.,Raushel, F.M.
Structure of diethyl phosphate bound to the binuclear metal center of phosphotriesterase.
Biochemistry, 47:9497-9504, 2008

PubMed 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.

PubMed: 18702530
DOI: 10.1021/bi800971v

Experimental method

X-RAY DIFFRACTION (1.83 Å)