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 

Starting Model: experimental
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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: https://doi.org/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 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Manganese-dependent inorganic pyrophosphatase
A, B
310Streptococcus agalactiae A909Mutation(s): 0 
Gene Names: ppaC
EC: 3.6.1.1
UniProt
Find proteins for Q3K0B5 (Streptococcus agalactiae serotype Ia (strain ATCC 27591 / A909 / CDC SS700))
Explore Q3K0B5 
Go to UniProtKB:  Q3K0B5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3K0B5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRP
Query on TRP

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B]
TRYPTOPHAN
C11 H12 N2 O2
QIVBCDIJIAJPQS-VIFPVBQESA-N
2PN
Query on 2PN

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
IMIDODIPHOSPHORIC ACID
H5 N O6 P2
GNGSOPFGGKKDQP-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
H [auth B],
I [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
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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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description