Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 60.36 kDa 
• Atom Count: 4613 
• Modelled Residue Count: 535 
• Deposited Residue Count: 540 
• Unique protein chains: 1

2OLR

Crystal structure of Escherichia coli phosphoenolpyruvate carboxykinase complexed with carbon dioxide, Mg2+, ATP

• PDB DOI: 10.2210/pdb2OLR/pdb

• Classification: LYASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2007-01-19 Released: 2007-06-12 
• Deposition Author(s): Cotelesage, J.J., Delbaere, L.T., Goldie, H., Puttick, J., Rajabi, B., Novakovski, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.198 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 

Literature

How does an enzyme recognize CO2?

Cotelesage, J.J., Puttick, J., Goldie, H., Rajabi, B., Novakovski, B., Delbaere, L.T.

(2007) Int J Biochem Cell Biol 39: 1204-1210

• PubMed: 17475535 
• DOI: 10.1016/j.biocel.2007.03.015
• Primary Citation of Related Structures:  
  2OLQ, 2OLR


• PubMed Abstract: 
  

Phosphoenolpyruvate carboxykinase (PCK) reversibly catalyzes the carboxylation of phosphoenolpyruvate to oxaloacetate. Carbon dioxide, and not bicarbonate ion, is the substrate utilized. Assays of the carboxylation reaction show that initial velocities are 7.6-fold higher when CO(2) is used instead of HCO(3)(-). Two Escherichia coli PCK-CO(2) crystal structures are presented here. The location of CO(2) is the same for both structures; however the orientation of CO(2) is significantly different, likely from the presence of a manganese ion in one of the structures. PCK and the other three known protein-CO(2) crystal structure complexes have been compared; all have CO(2) hydrogen bonding with a basic amino acid side chain (Arg65 or Lys213 in PCK), likely to polarize CO(2) to make the central carbon atom more electrophilic and thus more reactive. Kinetic studies found that the PCK mutant Arg65Gln increased the K(M) for substrates PEP and oxaloacetate but not for CO(2). The unchanged K(M) for CO(2) can be explained since the Arg65Gln mutant likely maintains a hydrogen bond to one of the oxygen atoms of carbon dioxide.

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Organizational Affiliation: 

Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Sask., Canada.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoenolpyruvate carboxykinase	A	540	Escherichia coli K-12	Mutation(s): 0  Gene Names: pckA, pck, b3403, JW3366 EC: 4.1.1.49
UniProt
Find proteins for P22259 (Escherichia coli (strain K12)) Explore P22259  Go to UniProtKB:  P22259

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	F [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
CO2	D [auth A], E [auth A]	CARBON DIOXIDE C O2 CURLTUGMZLYLDI-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.198 
• R-Value Work: 0.175 
• R-Value Observed: 0.176 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.854	α = 90
b = 95.564	β = 96.3
c = 46.476	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-01-19 
• Released Date: 2007-06-12 
Deposition Author(s): Cotelesage, J.J., Delbaere, L.T., Goldie, H., Puttick, J., Rajabi, B., Novakovski, B.

Revision History  

• Version 1.0: 2007-06-12
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model