Pyruvate Phosphate Dikinase with Bound Mg-phosphonopyruvate

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.198 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


Pyruvate site of pyruvate phosphate dikinase: crystal structure of the enzyme-phosphonopyruvate complex, and mutant analysis

Herzberg, O.Chen, C.C.Liu, S.Tempczyk, A.Howard, A.Wei, M.Ye, D.Dunaway-Mariano, D.

(2002) Biochemistry 41: 780-787

  • DOI: https://doi.org/10.1021/bi011799+
  • Primary Citation of Related Structures:  
    1KBL, 1KC7

  • PubMed Abstract: 

    Crystals of pyruvate phosphate dikinase in complex with a substrate analogue inhibitor, phosphonopyruvate (K(i) = 3 microM), have been obtained in the presence of Mg(2+). The structure has been determined and refined at 2.2 A resolution, revealing that the Mg(2+)-bound phosphonopyruvate binds in the alpha/beta-barrel's central channel, at the C-termini of the beta-strands. The mode of binding resembles closely the previously proposed PEP substrate binding mode, inferred by the homology of the structure (but not sequence homology) to pyruvate kinase. Kinetic analysis of site-directed mutants, probing residues involved in inhibitor binding, showed that all mutations resulted in inactivation, confirming the key role that these residues play in catalysis. Comparison between the structure of the PPDK-phosphonopyruvate complex and the structures of two complexes of pyruvate kinase, one with Mg(2+)-bound phospholactate and the other with Mg(2+)-oxalate and ATP, revealed that the two enzymes share some key features that facilitate common modes of substrate binding. There are also important structural differences; most notably, the machinery for acid/base catalysis is different.

  • Organizational Affiliation

    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600 Gudelsky Drive, Rockville, Maryland 20850, USA. osnat@carb.nist.gov

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
pyruvate phosphate dikinase873[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: 2.20 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.198 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.21α = 90
b = 58.42β = 94.99
c = 102.55γ = 90
Software Package:
Software NamePurpose
X-GENdata reduction
X-GENdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-01-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2023-08-16
    Changes: Data collection, Database references, Derived calculations, Refinement description