Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites.

Herzberg, O.Chen, C.C.Kapadia, G.McGuire, M.Carroll, L.J.Noh, S.J.Dunaway-Mariano, D.

(1996) Proc Natl Acad Sci U S A 93: 2652-2657

  • DOI: https://doi.org/10.1073/pnas.93.7.2652
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The crystal structure of pyruvate phosphate dikinase, a histidyl multiphosphotransfer enzyme that synthesizes adenosine triphosphate, reveals a three-domain molecule in which the phosphohistidine domain is flanked by the nucleotide and the phosphoenolpyruvate/pyruvate domains, with the two substrate binding sites approximately 45 angstroms apart. The modes of substrate binding have been deduced by analogy to D-Ala-D-Ala ligase and to pyruvate kinase. Coupling between the two remote active sites is facilitated by two conformational states of the phosphohistidine domain. While the crystal structure represents the state of interaction with the nucleotide, the second state is achieved by swiveling around two flexible peptide linkers. This dramatic conformational transition brings the phosphocarrier residue in close proximity to phosphoenolpyruvate/pyruvate. The swiveling-domain paradigm provides an effective mechanism for communication in complex multidomain/multiactive site proteins.

  • Organizational Affiliation

    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, 20850, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PYRUVATE PHOSPHATE DIKINASE874[Clostridium] symbiosumMutation(s): 0 
Gene Names: PPDK
Find proteins for P22983 (Clostridium symbiosum)
Explore P22983 
Go to UniProtKB:  P22983
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22983
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Work: 0.182 
  • R-Value Observed: 0.182 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.8α = 90
b = 58.8β = 94.8
c = 102γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
XENGENdata reduction

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1996-04-03
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations, Other