2iw4: Difference between revisions
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==Overview== | ==Overview== | ||
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 ... | 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. | ||
==About this Structure== | ==About this Structure== | ||
2IW4 is a | 2IW4 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis] with FE, MG, MN, SO4, 2PN, PG4 and GOL as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Inorganic_diphosphatase Inorganic diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.1 3.6.1.1] Structure known Active Site: AC1. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2IW4 OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: substrate complex]] | [[Category: substrate complex]] | ||
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Revision as of 14:18, 5 November 2007
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CRYSTAL STRUCTURE OF BASILLUS SUBTILIS FAMILY II INORGANIC PYROPHOSPHATASE MUTANT, H98Q, IN COMPLEX WITH PNP
OverviewOverview
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.
About this StructureAbout this Structure
2IW4 is a Single protein structure of sequence from Bacillus subtilis with FE, MG, MN, SO4, 2PN, PG4 and GOL as ligands. Active as Inorganic diphosphatase, with EC number 3.6.1.1 Structure known Active Site: AC1. Full crystallographic information is available from OCA.
ReferenceReference
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
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