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PDBsum entry 2fm4

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protein links
Transferase PDB id
2fm4
Jmol
Contents
Protein chain
128 a.a. *
* Residue conservation analysis
PDB id:
2fm4
Name: Transferase
Title: Nmr structure of the phosphoryl carrier domain of pyruvate phosphate dikinase
Structure: Pyruvate, phosphate dikinase. Chain: a. Synonym: pyruvate, orthophosphate dikinase. Engineered: yes
Source: Clostridium symbiosum. Organism_taxid: 1512. Gene: ppdk. Expressed in: escherichia coli. Expression_system_taxid: 562
NMR struc: 11 models
Authors: J.B.Ames
Key ref:
Y.Lin et al. (2006). Examination of the structure, stability, and catalytic potential in the engineered phosphoryl carrier domain of pyruvate phosphate dikinase. Biochemistry, 45, 1702-1711. PubMed id: 16460017 DOI: 10.1021/bi051816l
Date:
06-Jan-06     Release date:   03-Oct-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 Enzyme reactions 
   Enzyme class: E.C.2.7.9.1  - Pyruvate, phosphate dikinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + pyruvate + phosphate = AMP + phosphoenolpyruvate + diphosphate
ATP
+ pyruvate
+ phosphate
= AMP
+ 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     transferase activity, transferring phosphorus-containing groups     2 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi051816l Biochemistry 45:1702-1711 (2006)
PubMed id: 16460017  
 
 
Examination of the structure, stability, and catalytic potential in the engineered phosphoryl carrier domain of pyruvate phosphate dikinase.
Y.Lin, J.D.Lusin, D.Ye, D.Dunaway-Mariano, J.B.Ames.
 
  ABSTRACT  
 
Pyruvate phosphate dikinase (PPDK) is a multidomain protein that catalyzes the interconversion of ATP, pyruvate, and phosphate with AMP, phosphoenolpyruvate (PEP), and pyrophosphate using its central domain to transport phosphoryl groups between two distant active sites. In this study, the mechanism by which the central domain moves between the two catalytic sites located on the N-terminal and C-terminal domains was probed by expressing this domain as an independent protein and measuring its structure, stability, and ability to catalyze the ATP/phosphate partial reaction in conjunction with the engineered N-terminal domain protein (residues 1-340 of the native PPDK). The encoding gene was engineered to express the central domain as residues 381-512 of the native PPDK. The central domain was purified and shown to be soluble, monomeric (13,438 Da), and stable (deltaG = 4.3 kcal/mol for unfolding in buffer at pH 7.0, 25 degrees C) and to possess native structure, as determined by multidimensional heteronuclear NMR analysis. The main chain structure of the central domain in solution aligns closely with that of the X-ray structure of native PPDK (the root-mean-square deviation is 2.2 A). Single turnover reactions of [14C]ATP and phosphate, carried out in the presence of equal concentrations of central domain and the N-terminal domain protein, did not produce the expected products, in contrast to efficient product formation observed for the N-terminal central domain construct (residues 1-553 of the native PPDK). These results are interpreted as evidence that the central domain, although solvent-compatible, must be tethered by the flexible linkers to the N-terminal domain for the productive domain-domain docking required for efficient catalysis.