Crystal structure of E.coli phosphoenolpyruvate carboxylase in complex with Mn2+ and DCDP

Experimental Data Snapshot

  • Resolution: 2.35 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.195 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Crystal structures of C4 form maize and quaternary complex of E. coli phosphoenolpyruvate carboxylases.

Matsumura, H.Xie, Y.Shirakata, S.Inoue, T.Yoshinaga, T.Ueno, Y.Izui, K.Kai, Y.

(2002) Structure 10: 1721-1730

  • DOI: https://doi.org/10.1016/s0969-2126(02)00913-9
  • Primary Citation of Related Structures:  
    1JQN, 1JQO

  • PubMed Abstract: 

    Phosphoenolpyruvate carboxylase (PEPC) catalyzes the first step in the fixation of atmospheric CO(2) during C(4) photosynthesis. The crystal structure of C(4) form maize PEPC (ZmPEPC), the first structure of the plant PEPCs, has been determined at 3.0 A resolution. The structure includes a sulfate ion at the plausible binding site of an allosteric activator, glucose 6-phosphate. The crystal structure of E. coli PEPC (EcPEPC) complexed with Mn(2+), phosphoenolpyruvate analog (3,3-dichloro-2-dihydroxyphosphinoylmethyl-2-propenoate), and an allosteric inhibitor, aspartate, has also been determined at 2.35 A resolution. Dynamic movements were found in the ZmPEPC structure, compared with the EcPEPC structure, around two loops near the active site. On the basis of these molecular structures, the mechanisms for the carboxylation reaction and for the allosteric regulation of PEPC are proposed.

  • Organizational Affiliation

    Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
phosphoenolpyruvate carboxylase883Escherichia coliMutation(s): 0 
Gene Names: Escherichia coli
Find proteins for P00864 (Escherichia coli (strain K12))
Explore P00864 
Go to UniProtKB:  P00864
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00864
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.35 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.195 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.95α = 90
b = 249.06β = 90
c = 83.12γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-01-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-05-30
    Changes: Data collection, Derived calculations
  • Version 1.4: 2024-03-13
    Changes: Data collection, Database references, Derived calculations