2haw
From Proteopedia
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| - | [[Image:2haw.gif|left|200px]] | + | [[Image:2haw.gif|left|200px]] |
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| - | '''Crystal structure of family II Inorganic pyrophosphatase in complex with PNP''' | + | {{Structure |
| + | |PDB= 2haw |SIZE=350|CAPTION= <scene name='initialview01'>2haw</scene>, resolution 1.75Å | ||
| + | |SITE= | ||
| + | |LIGAND= <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=F:FLUORIDE+ION'>F</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=2PN:IMIDODIPHOSPHORIC+ACID'>2PN</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene> | ||
| + | |ACTIVITY= [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] | ||
| + | |GENE= | ||
| + | }} | ||
| + | |||
| + | '''Crystal structure of family II Inorganic pyrophosphatase in complex with PNP''' | ||
| + | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
| - | 2HAW is a [ | + | 2HAW is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2HAW OCA]. |
==Reference== | ==Reference== | ||
| - | 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:[http:// | + | 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:[http://www.ncbi.nlm.nih.gov/pubmed/17095506 17095506] |
[[Category: Bacillus subtilis]] | [[Category: Bacillus subtilis]] | ||
[[Category: Inorganic diphosphatase]] | [[Category: Inorganic diphosphatase]] | ||
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[[Category: substrate complex]] | [[Category: substrate complex]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 17:14:49 2008'' |
Revision as of 15:14, 20 March 2008
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| , resolution 1.75Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , and | ||||||
| Activity: | Inorganic diphosphatase, with EC number 3.6.1.1 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of family II Inorganic pyrophosphatase in complex with PNP
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 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
2HAW is a Single protein structure of sequence from Bacillus subtilis. Full crystallographic information is available from OCA.
Reference
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
Page seeded by OCA on Thu Mar 20 17:14:49 2008
Categories: Bacillus subtilis | Inorganic diphosphatase | Single protein | Fabrichniy, I P. | Goldman, A. | Lehtio, L. | Oksanen, E. | 1PE | 2PN | CL | F | GOL | MG | PG4 | SO4 | Hydrolase | Pyrophosphatase | Substrate complex
