Structure of Bacillus subtilis inorganic pyrophosphatase

Experimental Data Snapshot

  • Resolution: 2.05 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

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Structural Studies of Metal Ions in Family II Pyrophosphatases: The Requirement for a Janus Ion

Fabrichniy, I.P.Lehtio, L.Salminen, A.Zyryanov, A.B.Baykov, A.A.Lahti, R.Goldman, A.

(2004) Biochemistry 43: 14403-14411

  • DOI: https://doi.org/10.1021/bi0484973
  • Primary Citation of Related Structures:  
    1WPM, 1WPN, 1WPP

  • 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.

  • Organizational Affiliation

    Program in Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, P.O. Box 65, FIN-00014, Helsinki, Finland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Manganese-dependent inorganic pyrophosphatase
A, B
309Bacillus subtilisMutation(s): 0 
Find proteins for P37487 (Bacillus subtilis (strain 168))
Explore P37487 
Go to UniProtKB:  P37487
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP37487
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.05 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.675α = 90
b = 117.293β = 90
c = 144.989γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-23
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Derived calculations