1JQN

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

• PDB DOI:  https://doi.org/10.2210/pdb1JQN/pdb

• Classification: LYASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

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

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

• PubMed: 12467579 
• 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.

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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

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 99.6 kDa 
• Atom Count: 7,097 
• Modelled Residue Count: 874 
• Deposited Residue Count: 883 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
phosphoenolpyruvate carboxylase	A	883	Escherichia coli	Mutation(s): 0  Gene Names: Escherichia coli EC: 4.1.1.31
UniProt
Find proteins for P00864 (Escherichia coli (strain K12)) Explore P00864  Go to UniProtKB:  P00864

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCO	D [auth A]	3,3-DICHLORO-2-PHOSPHONOMETHYL-ACRYLIC ACID C4 H5 Cl2 O5 P IBGSKYLUHGAGLB-UHFFFAOYSA-N
ASP	C [auth A]	ASPARTIC ACID C4 H7 N O4 CKLJMWTZIZZHCS-REOHCLBHSA-N
MN	B [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

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 = 117.95	α = 90
b = 249.06	β = 90
c = 83.12	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• 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