3c86 | pdb_00003c86

OpdA from agrobacterium radiobacter with bound product diethyl thiophosphate from crystal soaking with tetraethyl dithiopyrophosphate- 1.8 A

spinqualitylabelsall models 3c86, resolution 1.80Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 3c86 is a 1 chain structure with sequence from Agrobacterium tumefaciens. This structure supersedes the now removed PDB entry 2r1o. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.8Å Ligands: CO, DPJ, EDO, FE2, KCX Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function Q93LD7_RHIRD Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMed The mechanism by which the binuclear metallophosphotriesterases (PTEs, E.C. 3.1.8.1) catalyse substrate hydrolysis has been extensively studied. The mu-hydroxo bridge between the metal ions has been proposed to be the initiating nucleophile in the hydrolytic reaction. In contrast, analysis of some biomimetic systems has indicated that mu-hydroxo bridges are often not themselves nucleophiles, but act as general bases for freely exchangeable nucleophilic water molecules. Herein, we present crystallographic analyses of a bacterial PTE from Agrobacterium radiobacter, OpdA, capturing the enzyme-substrate complex during hydrolysis. This model of the Michaelis complex suggests the alignment of the substrate will favour attack from a solvent molecule terminally coordinated to the alpha-metal ion. The bridging of both metal ions by the product, without disruption of the mu-hydroxo bridge, is also consistent with nucleophilic attack occurring from the terminal position. When phosphodiesters are soaked into crystals of OpdA, they coordinate bidentately to the beta-metal ion, displacing the mu-hydroxo bridge. Thus, alternative product-binding modes exist for the PTEs, and it is the bridging mode that appears to result from phosphotriester hydrolysis. Kinetic analysis of the PTE and promiscuous phosphodiesterase activities confirms that the presence of a mu-hydroxo bridge during phosphotriester hydrolysis is correlated with a lower pK(a) for the nucleophile, consistent with a general base function during catalysis. In crystallo capture of a Michaelis complex and product-binding modes of a bacterial phosphotriesterase.,Jackson CJ, Foo JL, Kim HK, Carr PD, Liu JW, Salem G, Ollis DL J Mol Biol. 2008 Feb 1;375(5):1189-96. Epub 2007 Nov 1. PMID:18082180 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Phosphotriesterase 3D structures

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