4RPA

Crystal structure of inorganic pyrophosphatase from Staphylococcus aureus in complex with Mn2+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structure of inorganic pyrophosphatase from Staphylococcus aureus reveals conformational flexibility of the active site.

Gajadeera, C.S.Zhang, X.Wei, Y.Tsodikov, O.V.

(2015) J Struct Biol 189: 81-86

  • DOI: https://doi.org/10.1016/j.jsb.2014.12.003
  • Primary Citation of Related Structures:  
    4RPA

  • PubMed Abstract: 

    Cytoplasmic inorganic pyrophosphatase (PPiase) is an enzyme essential for survival of organisms, from bacteria to human. PPiases are divided into two structurally distinct families: family I PPiases are Mg(2+)-dependent and present in most archaea, eukaryotes and prokaryotes, whereas the relatively less understood family II PPiases are Mn(2+)-dependent and present only in some archaea, bacteria and primitive eukaryotes. Staphylococcus aureus (SA), a dangerous pathogen and a frequent cause of hospital infections, contains a family II PPiase (PpaC), which is an attractive potential target for development of novel antibacterial agents. We determined a crystal structure of SA PpaC in complex with catalytic Mn(2+) at 2.1Å resolution. The active site contains two catalytic Mn(2+) binding sites, each half-occupied, reconciling the previously observed 1:1 Mn(2+):enzyme stoichiometry with the presence of two divalent metal ion sites in the apo-enzyme. Unexpectedly, despite the absence of the substrate or products in the active site, the two domains of SA PpaC form a closed active site, a conformation observed in structures of other family II PPiases only in complex with substrate or product mimics. A region spanning residues 295-298, which contains a conserved substrate binding RKK motif, is flipped out of the active site, an unprecedented conformation for a PPiase. Because the mutant of Arg295 to an alanine is devoid of activity, this loop likely undergoes an induced-fit conformational change upon substrate binding and product dissociation. This closed conformation of SA PPiase may serve as an attractive target for rational design of inhibitors of this enzyme.


  • Organizational Affiliation

    Department of Pharmaceutical Sciences, University of Kentucky, College of Pharmacy, 789 S. Limestone St., Lexington, KY 40536, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable manganese-dependent inorganic pyrophosphatase
A, B
317Staphylococcus aureusMutation(s): 0 
Gene Names: ppaC
EC: 3.6.1.1
UniProt
Find proteins for P65752 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Explore P65752 
Go to UniProtKB:  P65752
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP65752
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.406α = 90
b = 99.406β = 90
c = 425.285γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-04-08
    Changes: Database references
  • Version 1.2: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2023-12-06
    Changes: Data collection