1wpn: Difference between revisions
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'''Crystal structure of the N-terminal core of Bacillus subtilis inorganic pyrophosphatase''' | {{Structure | ||
|PDB= 1wpn |SIZE=350|CAPTION= <scene name='initialview01'>1wpn</scene>, resolution 1.30Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene> and <scene name='pdbligand=SO4:SULFATE ION'>SO4</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 the N-terminal core of Bacillus subtilis inorganic pyrophosphatase''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1WPN is a [ | 1WPN 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=1WPN OCA]. | ||
==Reference== | ==Reference== | ||
Structural studies of metal ions in family II pyrophosphatases: the requirement for a Janus ion., Fabrichniy IP, Lehtio L, Salminen A, Zyryanov AB, Baykov AA, Lahti R, Goldman A, Biochemistry. 2004 Nov 16;43(45):14403-11. PMID:[http:// | Structural studies of metal ions in family II pyrophosphatases: the requirement for a Janus ion., Fabrichniy IP, Lehtio L, Salminen A, Zyryanov AB, Baykov AA, Lahti R, Goldman A, Biochemistry. 2004 Nov 16;43(45):14403-11. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15533045 15533045] | ||
[[Category: Bacillus subtilis]] | [[Category: Bacillus subtilis]] | ||
[[Category: Inorganic diphosphatase]] | [[Category: Inorganic diphosphatase]] | ||
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[[Category: metal binding]] | [[Category: metal binding]] | ||
''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 15:00:02 2008'' | ||
Revision as of 16:00, 20 March 2008
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| , resolution 1.30Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | and | ||||||
| Activity: | Inorganic diphosphatase, with EC number 3.6.1.1 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Crystal structure of the N-terminal core of Bacillus subtilis inorganic pyrophosphatase
OverviewOverview
Family II inorganic pyrophosphatases (PPases) constitute a new evolutionary group of PPases, with a different fold and mechanism than the common family I enzyme; they are related to the "DHH" family of phosphoesterases. Biochemical studies have shown that Mn(2+) and Co(2+) preferentially activate family II PPases; Mg(2+) partially activates; and Zn(2+) can either activate or inhibit (Zyryanov et al., Biochemistry, 43, 14395-14402, accompanying paper in this issue). The three solved family II PPase structures did not explain the differences between the PPase families nor the metal ion differences described above. We therefore solved three new family II PPase structures: Bacillus subtilis PPase (Bs-PPase) dimer core bound to Mn(2+) at 1.3 A resolution, and, at 2.05 A resolution, metal-free Bs-PPase and Streptococcus gordonii (Sg-PPase) containing sulfate and Zn(2+). Comparison of the new and old structures of various family II PPases demonstrates why the family II enzyme prefers Mn(2+) or Co(2+), as an activator rather than Mg(2+). Both M1 and M2 undergo significant changes upon substrate binding, changing from five-coordinate to octahedral geometry. Mn(2+) and Co(2+), which readily adopt different coordination states and geometries, are thus favored. Combining our structures with biochemical data, we identified M2 as the high-affinity metal site. Zn(2+) activates in the M1 site, where octahedral geometry is not essential for catalysis, but inhibits in the M2 site, because it is unable to assume octahedral geometry but remains trigonal bipyramidal. Finally, we propose that Lys205-Gln81-Gln80 form a hydrophilic channel to speed product release from the active site.
About this StructureAbout this Structure
1WPN is a Single protein structure of sequence from Bacillus subtilis. Full crystallographic information is available from OCA.
ReferenceReference
Structural studies of metal ions in family II pyrophosphatases: the requirement for a Janus ion., Fabrichniy IP, Lehtio L, Salminen A, Zyryanov AB, Baykov AA, Lahti R, Goldman A, Biochemistry. 2004 Nov 16;43(45):14403-11. PMID:15533045
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