6COM

2.3A crystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Asp269Asn

• PDB DOI: https://doi.org/10.2210/pdb6COM/pdb

• Classification: LYASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2018-03-12 Released: 2018-04-04 
• Deposition Author(s): Sokaribo, A.S., Cotelesage, J.H., Novakovski, B., Goldie, H., Sanders, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.209 
• R-Value Work: 0.148 
• R-Value Observed: 0.153 

Literature

Kinetic and structural analysis of Escherichia coli phosphoenolpyruvate carboxykinase mutants.

Sokaribo, A., Novakovski, B.A.A., Cotelesage, J., White, A.P., Sanders, D., Goldie, H.

(2020) Biochim Biophys Acta Gen Subj 1864: 129517-129517

• PubMed: 31911238 
• DOI: https://doi.org/10.1016/j.bbagen.2020.129517
• Primary Citation of Related Structures:  
  6COM, 6V2L, 6V2M, 6V2N


• PubMed Abstract: 
  

  Phosphoenolpyruvate carboxykinase (PEPCK) is a metabolic enzyme in the gluconeogenesis pathway, where it catalyzes the reversible conversion of oxaloacetate (OAA) to phosphoenolpyruvate (PEP) and CO ₂ . The substrates for Escherichia coli PEPCK are OAA and MgATP, with Mn ²⁺ acting as a cofactor. Analysis of PEPCK structures have revealed amino acid residues involved in substrate/cofactor coordination during catalysis.

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Organizational Affiliation: 

Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada; Vaccine and Infectious Disease Organization, International Vaccine Center, Saskatoon, SK, Canada. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 60.37 kDa 
• Atom Count: 4,435 
• Modelled Residue Count: 526 
• Deposited Residue Count: 540 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoenolpyruvate carboxykinase (ATP)	A	540	Escherichia coli K-12	Mutation(s): 1  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 (Subject of Investigation/LOI)	B [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
PYR (Subject of Investigation/LOI)	C [auth A]	PYRUVIC ACID C3 H4 O3 LCTONWCANYUPML-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.209 
• R-Value Work: 0.148 
• R-Value Observed: 0.153 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.595	α = 90
b = 94.175	β = 94.77
c = 46.457	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-04-04 
Deposition Author(s): Sokaribo, A.S., Cotelesage, J.H., Novakovski, B., Goldie, H., Sanders, D.

Revision History  

• Version 1.0: 2018-04-04
  Type: Initial release
  
• Version 1.1: 2020-01-22
  Changes: Database references, Structure summary
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection