PDBsum entry 1buk

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protein ligands links
Phosphotransferase PDB id
Protein chain
869 a.a.
SO4 ×2
Waters ×44
Superseded by: 2dik 2dik
PDB id:
Name: Phosphotransferase
Title: R337a mutant of pyruvate phosphate dikinase
Structure: Pyruvate phosphate dikinase. Chain: null. Synonym: ppdk. Engineered: yes. Mutation: k337a. Biological_unit: dimer. Other_details: ph7.0, crystallization at 30c, data collection at room temp
Source: Clostridium symbiosum. Strain: jm 101. Plasmid: pacyc184d-12. Gene: ppdk. Expressed in: escherichia coli.
Biol. unit: Dimer (from PDB file)
2.50Å     R-factor:   0.185    
Authors: K.Huang,O.Herzberg
Key ref:
M.McGuire et al. (1998). Location of the phosphate binding site within Clostridium symbiosum pyruvate phosphate dikinase. Biochemistry, 37, 13463-13474. PubMed id: 9753432 DOI: 10.1021/bi980920i
03-Sep-98     Release date:   09-Sep-98    
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 2 residue positions (black crosses)

 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


DOI no: 10.1021/bi980920i Biochemistry 37:13463-13474 (1998)
PubMed id: 9753432  
Location of the phosphate binding site within Clostridium symbiosum pyruvate phosphate dikinase.
M.McGuire, K.Huang, G.Kapadia, O.Herzberg, D.Dunaway-Mariano.
Pyruvate phosphate dikinase (PPDK) catalyzes the interconversion of ATP, Pi, and pyruvate with AMP, PPi, and PEP in three partial reactions: (1) E + ATP --> E.ATP --> E-PP.AMP, (2) E-PP.AMP + Pi --> E-PP.AMP.Pi --> E-P.AMP.PPi, and (3) E-P + pyruvate --> E-P.pyruvate --> E.PEP. The Clostridium symbiosum PPDK structure consists of N-terminal, central, and C-terminal domains. The N-terminal and central domains catalyze partial reactions 1 and 2 whereas the C-terminal and central domains catalyze partial reaction 3. The goal of the present work is to determine where on the N-terminal domain catalysis of partial reactions 1 and 2 occurs and, in particular, where the Pi binding site is located. Computer modeling studies implicated Arg337 as a key residue for Pi binding. This role was tested by site-directed mutagenesis. The R337A PPDK was shown to be impaired in catalysis of the forward (kcat 300-fold lower) and reverse (kcat 30-fold lower) full reactions. Time courses for the single turnover reactions were measured to show that catalysis of partial reaction 1 is 5-fold slower in the mutant, catalysis of the second partial reaction is 140-fold slower in the mutant, and catalysis of the third partial reaction is unaffected. With the exception of the mutation site, the crystal structure of the R337A PPDK closely resembles the structure of the wild-type protein. Thus, the altered kinetic properties observed for this mutant are attributed solely to the elimination of the interaction between substrate and the guanidinium group of the Arg337 side chain. On the basis of these findings we propose that the Pi binding site is located within the crevice of the PPDK N-terminal domain, at a site that is flanked by the ATP beta-P and the Mg2+ cofactor.

Literature references that cite this PDB file's key reference

  PubMed id Reference
16400177 C.H.Slamovits, and P.J.Keeling (2006).
Pyruvate-phosphate dikinase of oxymonads and parabasalia and the evolution of pyrophosphate-dependent glycolysis in anaerobic eukaryotes.
  Eukaryot Cell, 5, 148-154.  
10715138 B.R.Howard, J.A.Endrizzi, and S.J.Remington (2000).
Crystal structure of Escherichia coli malate synthase G complexed with magnesium and glyoxylate at 2.0 A resolution: mechanistic implications.
  Biochemistry, 39, 3156-3168.
PDB code: 1d8c
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