5HRM

Crystal structure of phosphotriesterase from Sphingobium sp. TCM1

Summary for 5HRM

• Entry DOI: 10.2210/pdb5hrm/pdb
• Related: 5IOJ
• Descriptor: Haloalkylphosphorus hydrolase, MANGANESE (II) ION (3 entities in total)
• Functional Keywords: phosphotriesterase, hydrolase, beta-propeller, organophosphate degradation
• Biological source: Sphingobium sp. TCM1
• Total number of polymer chains: 4
• Total formula weight: 218413.32

Authors

Mabanglo, M.F.,Raushel, F.M. (deposition date: 2016-01-23, release date: 2016-07-13, Last modification date: 2024-11-06)

Primary citation

Mabanglo, M.F.,Xiang, D.F.,Bigley, A.N.,Raushel, F.M.
Structure of a Novel Phosphotriesterase from Sphingobium sp. TCM1: A Familiar Binuclear Metal Center Embedded in a Seven-Bladed beta-Propeller Protein Fold.
Biochemistry, 55:3963-3974, 2016

PubMed Abstract: A novel phosphotriesterase was recently discovered and purified from Sphingobium sp. TCM1 (Sb-PTE) and shown to catalyze the hydrolysis of a broad spectrum of organophosphate esters with a catalytic efficiency that exceeds 10(6) M(-1) s(-1) for the hydrolysis of triphenyl phosphate. The enzyme was crystallized and the three-dimensional structure determined to a resolution of 2.1 Å using single-wavelength anomalous diffraction (Protein Data Bank entry 5HRM ). The enzyme adopts a seven-bladed β-propeller protein fold, and three disulfide bonds were identified between Cys-146 and Cys-242, Cys-411 and Cys-443, and Cys-542 and Cys-559. The active site of Sb-PTE contains a binuclear manganese center that is nearly identical to that of the structurally unrelated phosphotriesterase from Pseudomonas diminuta (Pd-PTE). The two metal ions in the active site are bridged to one another by Glu-201 and a water molecule. The α-metal ion is further coordinated to the protein by interactions with His-389, His-475, and Glu-407, whereas the β-metal ion is further liganded to His-317 and His-258. Computational docking of mimics of the proposed pentavalent reaction intermediates for the hydrolysis of organophosphates was used to provide a model for the binding of chiral substrates in the active site of Sb-PTE. The most striking difference in the catalytic properties of Sb-PTE, relative to those of Pd-PTE, is the enhanced rate of hydrolysis of organophosphate esters with substantially weaker leaving groups. The structural basis for this difference in the catalytic properties between Sb-PTE and Pd-PTE, despite the nearly identical binuclear metal centers for the activation of the substrate and nucleophilic water molecule, is at present unclear.

PubMed: 27353520
DOI: 10.1021/acs.biochem.6b00364

Experimental method

X-RAY DIFFRACTION (2.051 Å)