1WPM

Structure of Bacillus subtilis inorganic pyrophosphatase

1WPM の概要

• エントリーDOI: 10.2210/pdb1wpm/pdb
• 関連するPDBエントリー: 1WPN 1WPP
• 分子名称: Manganese-dependent inorganic pyrophosphatase, SULFATE ION, TETRAETHYLENE GLYCOL, ... (4 entities in total)
• 機能のキーワード: inorganic pyrophosphatase, ppase, metal binding, hydrolase
• 由来する生物種: Bacillus subtilis
• 細胞内の位置: Cytoplasm: P37487
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 69018.40

構造登録者

Fabrichniy, I.P.,Lehtio, L.,Salminen, A.,Baykov, A.A.,Lahti, R.,Goldman, A. (登録日: 2004-09-09, 公開日: 2004-11-23, 最終更新日: 2024-03-13)

主引用文献

Fabrichniy, I.P.,Lehtio, L.,Salminen, A.,Zyryanov, A.B.,Baykov, A.A.,Lahti, R.,Goldman, A.
Structural Studies of Metal Ions in Family II Pyrophosphatases: The Requirement for a Janus Ion
Biochemistry, 43:14403-14411, 2004

PubMed Abstract: 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.

PubMed: 15533045
DOI: 10.1021/bi0484973

実験手法

X-RAY DIFFRACTION (2.05 Å)