2haw

Crystal structure of family II Inorganic pyrophosphatase in complex with PNP

spinqualitylabelsall models 2haw, resolution 1.75Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2haw is a 2 chain structure with sequence from "vibrio_subtilis"_ehrenberg_1835 "vibrio subtilis" ehrenberg 1835. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: 1PE, 2PN, CL, F, GOL, MG, PG4, SO4 Activity: Inorganic diphosphatase, with EC number 3.6.1.1 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT 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 We report the first crystal structures of a family II pyrophosphatase complexed with a substrate analogue, imidodiphosphate (PNP). These provide new insights into the catalytic reaction mechanism of this enzyme family. We were able to capture the substrate complex both by fluoride inhibition and by site-directed mutagenesis providing complementary snapshots of the Michaelis complex. Structures of both the fluoride-inhibited wild type and the H98Q variant of the PNP-Bacillus subtilis pyrophosphatase complex show a unique trinuclear metal center. Each metal ion coordinates a terminal oxygen on the electrophilic phosphate and a lone pair on the putative nucleophile, thus placing it in line with the scissile bond without any coordination by protein. The nucleophile moves further away from the electrophilic phosphorus site, to the opposite side of the trimetal plane, upon binding of substrate. In comparison with earlier product complexes, the side chain of Lys296 has swung in and so three positively charged side chains, His98, Lys205 and Lys296, now surround the bridging nitrogen in PNP. Finally, one of the active sites in the wild-type structure appears to show evidence of substrate distortion. Binding to the enzyme may thus strain the substrate and thus enhance the catalytic rate. A trimetal site and substrate distortion in a family II inorganic pyrophosphatase.,Fabrichniy IP, Lehtio L, Tammenkoski M, Zyryanov AB, Oksanen E, Baykov AA, Lahti R, Goldman A J Biol Chem. 2007 Jan 12;282(2):1422-31. Epub 2006 Nov 8. PMID:17095506 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Inorganic pyrophosphatase 3D structures

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