1kc7 Summary

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Pyruvate Phosphate Dikinase with Bound Mg-phosphonopyruvate

The structure was published by Herzberg, O., Chen, C.C., Liu, S., et al., Wei, M., Ye, D., and Dunaway-Mariano, D., in 2002 in a paper entitled "Pyruvate site of pyruvate phosphate dikinase: crystal structure of the enzyme-phosphonopyruvate complex, and mutant analysis" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.2 Å and deposited in 2001.

The experimental data on which the structure is based was also deposited.

The PDB entry contains the structure of pyruvate phosphate dikinase. This molecule has the UniProt identifier P22983 (PPDK_CLOSY)search. The sample contained 873 residues which is 100% of the natural sequence. Out of 873 residues 872 were observed and are deposited in the PDB.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

The molecule has more than one probable quaternary state observed. For more details see the quaternary structure page.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A pyruvate phosphate dikinase P22983 (2-874) (PPDK_CLOSY)search [Clostridium] symbiosumsearch 100% 873 99%


This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
P22983 (2 - 874) pyruvate phosphate dikinase [Clostridium] symbiosum

Chain Structural classification (SCOP) Structural classification (CATH) Sequence family (Pfam)
A (P22983) Pyruvate phosphate dikinase, C-terminal domainsearch, Pyruvate phosphate dikinase, central domainsearch, Pyruvate phosphate dikinase, N-terminal domainsearch ATP-grasp fold, A domainsearch, Pyruvate Phosphate Dikinase, domain 2search, Phosphohistidine domains of PEP-utilising enzymessearch, Phosphoenolpyruvate-binding domainssearch, Acyl-CoA Binding Proteinsearch, ATP-grasp fold, B domainsearch PF00391: PEP-utilising enzyme, mobile domainsearch, PF01326: Pyruvate phosphate dikinase, PEP/pyruvate binding domainsearch, PF02896: PEP-utilising enzyme, TIM barrel domainsearch

Chain ID Molecular function (GO) Biological process (GO)
A (P22983) ATP bindingsearch transferase activity, transferring phosphorus-containing groupssearch transferase activitysearch kinase activitysearch catalytic activitysearch pyruvate, phosphate dikinase activitysearch nucleotide bindingsearch metal ion bindingsearch phosphorylationsearch pyruvate metabolic processsearch

Chain InterPro annotation
A PEP-utilising enzyme, C-terminalsearch Pyruvate phosphate dikinase, PEP/pyruvate-bindingsearch PEP-utilising enzyme, mobile domainsearch Pyruvate, phosphate dikinasesearch ATP-grasp fold, subdomain 1search ATP-grasp fold, subdomain 2search Pyruvate/Phosphoenolpyruvate kinase-like domainsearch PEP-utilising enzyme, active sitesearch PEP-utilising enzyme, conserved sitesearch