2ENX

Structure of the family II inorganic pyrophosphatase from Streptococcus agalactiae at 2.8 resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.196 

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This is version 1.2 of the entry. See complete history. 


Literature

Structure of the Streptococcus agalactiae family II inorganic pyrophosphatase at 2.80 A resolution

Rantanen, M.K., Lehtio, L., Rajagopal, L., Rubens, C.E., Goldman, A.

(2007) Acta Crystallogr D Biol Crystallogr 63: 738-743

  • DOI: 10.1107/S0907444907019695
  • Primary Citation of Related Structures:  
    2ENX

  • PubMed Abstract: 

    • Streptococcus agalactiae, a prokaryote that causes infections in neonates and immunocompromised adults, has a serine/threonine protein kinase (STK) signalling cascade. The structure of one of the targets, a family II inorganic pyrophosphatase, has been s ...

    Streptococcus agalactiae, a prokaryote that causes infections in neonates and immunocompromised adults, has a serine/threonine protein kinase (STK) signalling cascade. The structure of one of the targets, a family II inorganic pyrophosphatase, has been solved by molecular replacement and refined at 2.80 A resolution to an R factor of 19.2% (R(free) = 26.7%). The two monomers in the asymmetric unit are related by a noncrystallographic twofold axis, but the biological dimer is formed by a crystallographic twofold. Each monomer contains the pyrophosphate analogue imidodiphosphate (PNP) and three metal ions per active site: two Mn(2+) ions in sites M1 and M2 and an Mg(2+) ion in site M3. The enzyme is in the closed conformation. Like other family II enzymes, the structure consists of two domains (residues 1-191 and 198-311), with the active site located between them. The conformation of Lys298 in the active site is different from those observed previously and it coordinates to the conserved DHH motif in a unique way. The structure suggests that Ser150, Ser194, Ser195 and Ser296 are the most likely targets for the Ser/Thr kinase and phosphatase because they are surface-accessible and either in the active site or in the hinge region between the two domains.

    Organizational Affiliation: 

    Institute of Biotechnology, University of Helsinki, PO Box 65, Helsinki, FIN-00014, Finland.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Manganese-dependent inorganic pyrophosphatase A, B310Streptococcus agalactiae A909Mutation(s): 0 
Gene Names: ppaC, SAK_1430
EC: 3.6.1.1
Find proteins for Q3K0B5 (Streptococcus agalactiae serotype Ia (strain ATCC 27591 / A909 / CDC SS700))
Explore Q3K0B5 
Go to UniProtKB:  Q3K0B5
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.196 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 181.96α = 90
b = 181.96β = 90
c = 132.61γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-29
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance