Crystal Structure of Escherichia coli Polyphosphate Kinase

Experimental Data Snapshot

  • Resolution: 3.00 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.265 

wwPDB Validation   3D Report Full Report

This is version 1.5 of the entry. See complete history


Crystal structure of a polyphosphate kinase and its implications for polyphosphate synthesis

Zhu, Y.Huang, W.Lee, S.S.Xu, W.

(2005) EMBO Rep 6: 681-687

  • DOI: https://doi.org/10.1038/sj.embor.7400448
  • Primary Citation of Related Structures:  
    1XDO, 1XDP

  • PubMed Abstract: 

    Polyphosphate (polyP), a linear polymer of hundreds of orthophosphate residues, exists in all tested cells in nature, from pathogenic bacteria to mammals. In bacteria, polyP has a crucial role in stress responses and stationary-phase survival. Polyphosphate kinase (PPK) is the principal enzyme that catalyses the synthesis of polyP in bacteria. It has been shown that PPK is required for bacterial motility, biofilm formation and the production of virulence factors. PPK inhibitors may thus provide a unique therapeutic opportunity against antibiotic-resistant pathogens. Here, we report crystal structures of full-length Escherichia coli PPK and its complex with AMPPNP (beta-gamma-imidoadenosine 5-phosphate). PPK forms an interlocked dimer, with each 80 kDa monomer containing four structural domains. The PPK active site is located in a tunnel, which contains a unique ATP-binding pocket and may accommodate the translocation of synthesized polyP. The PPK structure has laid the foundation for understanding the initiation of polyP synthesis by PPK.

  • Organizational Affiliation

    Department of Biological Structure, Box 357420, University of Washington, Seattle, Washington 98195, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyphosphate kinase
A, B
687Escherichia coliMutation(s): 0 
Gene Names: ppk
Find proteins for P0A7B1 (Escherichia coli (strain K12))
Explore P0A7B1 
Go to UniProtKB:  P0A7B1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7B1
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.00 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.265 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154α = 90
b = 154β = 90
c = 155γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-06-21
    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: 2014-11-19
    Changes: Other
  • Version 1.4: 2021-07-28
    Changes: Refinement description
  • Version 1.5: 2023-08-23
    Changes: Data collection, Database references, Refinement description