PDBsum entry 1ggo

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protein ligands links
Transferase PDB id
Protein chain
869 a.a. *
SO4 ×2
Waters ×227
* Residue conservation analysis
PDB id:
Name: Transferase
Title: T453a mutant of pyruvate, phosphate dikinase
Structure: Protein (pyruvate, phosphate dikinase). Chain: a. Synonym: ppdk. Engineered: yes. Mutation: yes
Source: Clostridium symbiosum. Organism_taxid: 1512. Strain: jm 101. Gene: ppdk. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
2.60Å     R-factor:   0.177     R-free:   0.294
Authors: Z.Li,O.Herzberg
Key ref:
M.Wei et al. (2000). Identification of domain-domain docking sites within Clostridium symbiosum pyruvate phosphate dikinase by amino acid replacement. J Biol Chem, 275, 41156-41165. PubMed id: 10995759 DOI: 10.1074/jbc.M006149200
29-Aug-00     Release date:   10-Jan-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P22983  (PPDK_CLOSY) -  Pyruvate, phosphate dikinase
874 a.a.
869 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Pyruvate, phosphate dikinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + pyruvate + phosphate = AMP + phosphoenolpyruvate + diphosphate
+ pyruvate
+ phosphate
+ phosphoenolpyruvate
+ diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     phosphorylation   2 terms 
  Biochemical function     catalytic activity     8 terms  


DOI no: 10.1074/jbc.M006149200 J Biol Chem 275:41156-41165 (2000)
PubMed id: 10995759  
Identification of domain-domain docking sites within Clostridium symbiosum pyruvate phosphate dikinase by amino acid replacement.
M.Wei, Z.Li, D.Ye, O.Herzberg, D.Dunaway-Mariano.
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.
  Selected figure(s)  
Figure 2.
Fig. 2. Front and back views of the space filling models of the PPDK conformers 1 and 2 of Fig. 1 are shown to illustrate the conservation of residues at the domain-domain interface regions. The dark green, dark blue, and gold residues are stringently conserved among the 17 known PPDK sequences, while the pastel blue, pastel green, and yellow residues are variable.
Figure 3.
Fig. 3. A stereoview of the Arg219-Glu434/Glu437 and Glu271-Met452/Thr453 docking sites (a) and the Ser262-Ala^398 and Lys149-Glu430 interactions at the interface of the N-terminal and central domains (b). The N-terminal domain interface is shown in green, the central domain interface in yellow, and the domain linkers in pink. The ATP ligand is blue, the P[i] ligand red, the Mg(II) ion is magenta, and the catalytic His455 is black.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 41156-41165) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19801641 A.E.Oberholzer, P.Schneider, C.Siebold, U.Baumann, and B.Erni (2009).
Crystal structure of enzyme I of the phosphoenolpyruvate sugar phosphotransferase system in the dephosphorylated state.
  J Biol Chem, 284, 33169-33176.
PDB code: 2wqd
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