1QB4

CRYSTAL STRUCTURE OF MN(2+)-BOUND PHOSPHOENOLPYRUVATE CARBOXYLASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 93-96


  • PubMed Abstract: 
  • We have determined the crystal structure of Mn2+-bound Escherichia coli phosphoenolpyruvate carboxylase (PEPC) using X-ray diffraction at 2.6 A resolution, and specified the location of enzyme-bound Mn2+, which is essential for catalytic activity. Th ...

    We have determined the crystal structure of Mn2+-bound Escherichia coli phosphoenolpyruvate carboxylase (PEPC) using X-ray diffraction at 2.6 A resolution, and specified the location of enzyme-bound Mn2+, which is essential for catalytic activity. The electron density map reveals that Mn2+ is bound to the side chain oxygens of Glu-506 and Asp-543, and located at the top of the alpha/beta barrel in PEPC. The coordination sphere of Mn2+ observed in E. coli PEPC is similar to that of Mn2+ found in the pyruvate kinase structure. The model study of Mn2+-bound PEPC complexed with phosphoenolpyruvate (PEP) reveals that the side chains of Arg-396, Arg-581 and Arg-713 could interact with PEP.


    Related Citations: 
    • 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, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHOSPHOENOLPYRUVATE CARBOXYLASE
A
883Escherichia coli (strain K12)Gene Names: ppc (glu)
EC: 4.1.1.31
Find proteins for P00864 (Escherichia coli (strain K12))
Go to UniProtKB:  P00864
Small Molecules
Ligands 2 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
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: 2.6 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.223 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 117.750α = 90.00
b = 248.410β = 90.00
c = 83.470γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-05-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance