PDBsum entry 1kc7

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protein ligands metals links
Transferase PDB id
Protein chain
872 a.a. *
SO4 ×4
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Pyruvate phosphate dikinase with bound mg-phosphonopyruvate
Structure: Pyruvate phosphate dikinase. Chain: a. Synonym: ppdk. Engineered: yes
Source: Clostridium symbiosum. Organism_taxid: 1512. Gene: ppdk. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
2.20Å     R-factor:   0.198     R-free:   0.269
Authors: C.C.Chen,A.Howard,O.Herzberg
Key ref:
O.Herzberg et al. (2002). Pyruvate site of pyruvate phosphate dikinase: crystal structure of the enzyme-phosphonopyruvate complex, and mutant analysis. Biochemistry, 41, 780-787. PubMed id: 11790099 DOI: 10.1021/bi011799+
07-Nov-01     Release date:   30-Jan-02    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P22983  (PPDK_CLOSY) -  Pyruvate, phosphate dikinase
874 a.a.
872 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Pyruvate, phosphate dikinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + pyruvate + phosphate = AMP + phosphoenolpyruvate + diphosphate
Bound ligand (Het Group name = PPR)
matches with 60.00% similarity
+ 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: 10.1021/bi011799+ Biochemistry 41:780-787 (2002)
PubMed id: 11790099  
Pyruvate site of pyruvate phosphate dikinase: crystal structure of the enzyme-phosphonopyruvate complex, and mutant analysis.
O.Herzberg, C.C.Chen, S.Liu, A.Tempczyk, A.Howard, M.Wei, D.Ye, D.Dunaway-Mariano.
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.

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
18041759 B.Seebeck, I.Reulecke, A.Kämper, and M.Rarey (2008).
Modeling of metal interaction geometries for protein-ligand docking.
  Proteins, 71, 1237-1254.  
17053069 A.Teplyakov, K.Lim, P.P.Zhu, G.Kapadia, C.C.Chen, J.Schwartz, A.Howard, P.T.Reddy, A.Peterkofsky, and O.Herzberg (2006).
Structure of phosphorylated enzyme I, the phosphoenolpyruvate:sugar phosphotransferase system sugar translocation signal protein.
  Proc Natl Acad Sci U S A, 103, 16218-16223.
PDB code: 2hwg
16581832 E.Hurtado-Gómez, G.Fernández-Ballester, H.Nothaft, J.Gómez, F.Titgemeyer, and J.L.Neira (2006).
Biophysical characterization of the enzyme I of the Streptomyces coelicolor phosphoenolpyruvate:sugar phosphotransferase system.
  Biophys J, 90, 4592-4604.  
16547354 H.V.Patel, K.A.Vyas, R.L.Mattoo, M.Southworth, F.B.Perler, D.Comb, and S.Roseman (2006).
Properties of the C-terminal domain of enzyme I of the Escherichia coli phosphotransferase system.
  J Biol Chem, 281, 17579-17587.  
16867985 J.Márquez, S.Reinelt, B.Koch, R.Engelmann, W.Hengstenberg, and K.Scheffzek (2006).
Structure of the full-length enzyme I of the phosphoenolpyruvate-dependent sugar phosphotransferase system.
  J Biol Chem, 281, 32508-32515.
PDB code: 2hro
16936061 O.V.Mavrodi, D.V.Mavrodi, D.M.Weller, and L.S.Thomashow (2006).
Role of ptsP, orfT, and sss recombinase genes in root colonization by Pseudomonas fluorescens Q8r1-96.
  Appl Environ Microbiol, 72, 7111-7122.  
15485834 M.Varela-Gómez, R.Moreno-Sánchez, J.P.Pardo, and R.Perez-Montfort (2004).
Kinetic mechanism and metabolic role of pyruvate phosphate dikinase from Entamoeba histolytica.
  J Biol Chem, 279, 54124-54130.  
15229886 N.Fernandez-Fuentes, A.Hermoso, J.Espadaler, E.Querol, F.X.Aviles, and B.Oliva (2004).
Classification of common functional loops of kinase super-families.
  Proteins, 56, 539-555.  
12837791 F.Schmitzberger, A.G.Smith, C.Abell, and T.L.Blundell (2003).
Comparative analysis of the Escherichia coli ketopantoate hydroxymethyltransferase crystal structure confirms that it is a member of the (betaalpha)8 phosphoenolpyruvate/pyruvate superfamily.
  J Bacteriol, 185, 4163-4171.  
12931002 M.N.Dimitrova, A.Peterkofsky, and A.Ginsburg (2003).
Opposing effects of phosphoenolpyruvate and pyruvate with Mg(2+) on the conformational stability and dimerization of phosphotransferase enzyme I from Escherichia coli.
  Protein Sci, 12, 2047-2056.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.