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

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

  • 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
    • 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 U S A 96: 823
    • 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 D Biol Crystallogr 55: 1937

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
phosphoenolpyruvate carboxylaseA883Escherichia coliMutation(s): 0 
Gene Names: Escherichia coli
EC: 4.1.1.31
Find proteins for P00864 (Escherichia coli (strain K12))
Explore P00864 
Go to UniProtKB:  P00864
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DCO
Query on DCO

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 CCD File 
A
ASPARTIC ACID
C4 H7 N O4
CKLJMWTZIZZHCS-REOHCLBHSA-N
 Ligand Interaction
MN
Query on MN

Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-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 = 117.95α = 90
b = 249.06β = 90
c = 83.12γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

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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
    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