1JQN

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

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

  • Primary Citation of Related Structures:  

  • 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. ...

    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.


    Related Citations: 
    • Plausible phosphoenolpyruvate binding site revealed by 2.6 A structure of Mn2+-bound phosphoenolpyruvate carboxylase from Escherichia coli.
      Matsumura, H.,Terada, M.,Shirakata, S.,Inoue, T.,Yoshinaga, T.,Izui, K.,Kai, Y.
      (1999) FEBS Lett. 458: 93
    • Crystallization and preliminary x-ray diffraction studies of C4-form phosphoenolpyruvate carboxylase from maize diffraction studies of C4-form phosphoenolpyruvate carboxylase from maize.
      Matsumura, H.,Nagata, T.,Terada, M.,Shirakata, S.,Inoue, T.,Yoshinaga, T.,Ueno, Y.,Saze, H.,Izui, K.,Kai, Y.
      (1999) Acta Crystallogr.,Sect.D 55: 1937
    • Three-dimensional structure of phosphoenolpyruvate carboxylase: a proposed mechanism for allosteric inhibition
      Kai, Y.,Matsumura, H.,Inoue, T.,Terada, K.,Nagara, Y.,Yoshinaga, T.,Kihara, A.,Tsumura, K.,Izui, K.
      (1999) Proc.Natl.Acad.Sci.USA 96: 823


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
phosphoenolpyruvate carboxylase
A
883Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ppc (glu)
EC: 4.1.1.31
Find proteins for P00864 (Escherichia coli (strain K12))
Go to UniProtKB:  P00864
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
DCO
Query on DCO

Download SDF File 
Download CCD File 
A
3,3-DICHLORO-2-PHOSPHONOMETHYL-ACRYLIC ACID
C4 H5 Cl2 O5 P
IBGSKYLUHGAGLB-UHFFFAOYSA-N
 Ligand Interaction
ASP
Query on ASP

Download SDF File 
Download CCD File 
A
ASPARTIC ACID
C4 H7 N O4
CKLJMWTZIZZHCS-REOHCLBHSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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 = 117.950α = 90.00
b = 249.060β = 90.00
c = 83.120γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2001-08-07 
  • Released Date: 2003-01-14 
  • Deposition Author(s): Matsumura, H., Kai, Y.

Revision History 

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