6V2L

E. coli Phosphoenolpyruvate carboxykinase S250A

• PDB DOI:  https://doi.org/10.2210/pdb6V2L/pdb
• Entry: 6V2L supersedes: 6D5I

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


• Deposited: 2019-11-25 Released: 2019-12-11 
• Deposition Author(s): Sokaribo, A.S., Goldie, H., Sanders, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.208 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 

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. 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)

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content

• Total Structure Weight: 60.42 kDa 
• Atom Count: 4,710 
• Modelled Residue Count: 532 
• 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	Mutation(s): 1  Gene Names: pckA, D9G24_04840 EC: 4.1.1.49
UniProt
Find proteins for P22259 (Escherichia coli (strain K12)) Explore P22259  Go to UniProtKB:  P22259

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	B [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
ACT	C [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MN	D [auth A], E [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 0.208 
• R-Value Work: 0.167 
• R-Value Observed: 0.169 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.91	α = 90
b = 94.62	β = 96.21
c = 46.35	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-12-11 
Deposition Author(s): Sokaribo, A.S., Goldie, H., Sanders, D.
• This entry supersedes: 6D5I

Revision History  

• Version 1.0: 2019-12-11
  Type: Initial release
  
• Version 1.1: 2020-01-22
  Changes: Database references