1JQO

Crystal structure of C4-form phosphoenolpyruvate carboxylase from maize


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.236 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    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 ...

    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)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
phosphoenolpyruvate carboxylaseA, B970Zea maysMutation(s): 0 
Gene Names: PEP1PPC
EC: 4.1.1.31
UniProt
Find proteins for P04711 (Zea mays)
Explore P04711 
Go to UniProtKB:  P04711
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04711
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.236 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 158.44α = 90
b = 174.61β = 90
c = 254.28γ = 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  (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: Derived calculations, Version format compliance