1wpp
From Proteopedia
(New page: 200px<br /><applet load="1wpp" size="450" color="white" frame="true" align="right" spinBox="true" caption="1wpp, resolution 2.05Å" /> '''Structure of Strepto...) |
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| - | [[Image:1wpp.jpg|left|200px]]<br /><applet load="1wpp" size=" | + | [[Image:1wpp.jpg|left|200px]]<br /><applet load="1wpp" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1wpp, resolution 2.05Å" /> | caption="1wpp, resolution 2.05Å" /> | ||
'''Structure of Streptococcus gordonii inorganic pyrophosphatase'''<br /> | '''Structure of Streptococcus gordonii inorganic pyrophosphatase'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Family II inorganic pyrophosphatases (PPases) constitute a new | + | 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 Structure== | ==About this Structure== | ||
| - | 1WPP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptococcus_gordonii_str._challis Streptococcus gordonii str. challis] with ZN, SO4 and CL 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] Full crystallographic information is available from [http:// | + | 1WPP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Streptococcus_gordonii_str._challis Streptococcus gordonii str. challis] with <scene name='pdbligand=ZN:'>ZN</scene>, <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=CL:'>CL</scene> 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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WPP OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Streptococcus gordonii str. challis]] | [[Category: Streptococcus gordonii str. challis]] | ||
| - | [[Category: Baykov, A | + | [[Category: Baykov, A A.]] |
| - | [[Category: Fabrichniy, I | + | [[Category: Fabrichniy, I P.]] |
[[Category: Goldman, A.]] | [[Category: Goldman, A.]] | ||
[[Category: Lahti, R.]] | [[Category: Lahti, R.]] | ||
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[[Category: metal binding]] | [[Category: metal binding]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:46:54 2008'' |
Revision as of 13:46, 21 February 2008
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Structure of Streptococcus gordonii inorganic pyrophosphatase
Overview
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 Structure
1WPP is a Single protein structure of sequence from Streptococcus gordonii str. challis with , and as ligands. Active as Inorganic diphosphatase, with EC number 3.6.1.1 Full crystallographic information is available from OCA.
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:15533045
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