1WPN

Crystal structure of the N-terminal core of Bacillus subtilis inorganic pyrophosphatase

Summary for 1WPN

• Entry DOI: 10.2210/pdb1wpn/pdb
• Related: 1WPM 1WPP
• Descriptor: Manganese-dependent inorganic pyrophosphatase, MANGANESE (II) ION, SULFATE ION, ... (4 entities in total)
• Functional Keywords: inorganic pyrophosphatase, metal binding, hydrolase
• Biological source: Bacillus subtilis
• Cellular location: Cytoplasm: P37487
• Total number of polymer chains: 2
• Total formula weight: 42239.03

Authors

Fabrichniy, I.P.,Lehtio, L.,Salminen, A.,Baykov, A.A.,Lahti, R.,Goldman, A. (deposition date: 2004-09-09, release date: 2004-11-23, Last modification date: 2024-03-13)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.3 Å)