Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 

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This is version 1.5 of the entry. See complete history


Identification of domain-domain docking sites within Clostridium symbiosum pyruvate phosphate dikinase by amino acid replacement.

Wei, M.Li, Z.Ye, D.Herzberg, O.Dunaway-Mariano, D.

(2000) J Biol Chem 275: 41156-41165

  • DOI: https://doi.org/10.1074/jbc.M006149200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Potential domain-domain docking residues, identified from the x-ray structure of the Clostridium symbiosum apoPPDK, were replaced by site-directed mutagenesis. The steady-state and transient kinetic properties of the mutant enzymes were determined as a way of evaluating docking efficiency. PPDK mutants, in which one of two stringently conserved docking residues located on the N-terminal domain (Arg(219) and Glu(271)) was substituted, displayed largely unimpeded catalysis of the phosphoenolpyruvate partial reaction at the C-terminal domain, but significantly impaired catalysis (>10(4)) of the ATP pyrophosphorylation of His(455) at the N-terminal domain. In contrast, alanine mutants of two potential docking residues located on the N-terminal domain (Ser(262) and Lys(149)), which are not conserved among the PPDKs, exhibited essentially normal catalytic turnover. Arg(219) and Glu(271) were thus proposed to play an important role in guiding the central domain and, hence, the catalytic His(455) into position for catalysis. Substitution of central domain residues Glu(434)/Glu(437) and Thr(453), the respective docking partners of Arg(219) and Glu(271), resulted in mutants impaired in catalysis at the ATP active site. The x-ray crystal structure of the apo-T453A PPDK mutant was determined to test for possible misalignment of residues at the N-terminal domain-central domain interface that might result from loss of the Thr(453)-Glu(271) binding interaction. With the exception of the mutation site, the structure of T453A PPDK was found to be identical to that of the wild-type enzyme. It is hypothesized that the two Glu(271) interfacial binding sites that remain in the T453A PPDK mutant, Thr(453) backbone NH and Met(452) backbone NH, are sufficient to stabilize the native conformation as observed in the crystalline state but may be less effective in populating the reactive conformation in solution.

  • Organizational Affiliation

    Department of Chemistry, University of New Mexico, Albuquerque, New Mexico 87131, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (PYRUVATE, PHOSPHATE DIKINASE)873[Clostridium] symbiosumMutation(s): 1 
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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 
  • Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.73α = 90
b = 58.66β = 95.58
c = 102.78γ = 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: 2001-01-10
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2018-06-27
    Changes: Data collection, Database references
  • Version 1.5: 2023-12-27
    Changes: Data collection, Database references, Derived calculations