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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1016/j.jsb.2014.12.003
  • Structures With Same Primary Citation

  • 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, e ...

    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. Electronic address: oleg.tsodikov@uky.edu.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable manganese-dependent inorganic pyrophosphatase
A, B
317Staphylococcus aureusMutation(s): 0 
Gene Names: ppaC
EC: 3.6.1.1
Find proteins for P65752 (Staphylococcus aureus (strain Mu50 / ATCC 700699))
Go to UniProtKB:  P65752
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download CCD File 
A, B
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
A,BL-PEPTIDE LINKINGC3 H7 N O3 SCYS
OCS
Query on OCS
A,BL-PEPTIDE LINKINGC3 H7 N O5 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.222 
  • Space Group: P 61 2 2
  • Diffraction Data DOI: 10.15785/SBGRID/22 SBGrid
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-04-08
    Changes: Database references