6V2N

Crystal structure of E. coli phosphoenolpyruvate carboxykinase mutant Lys254Ser

PDB DOI: https://doi.org/10.2210/pdb6V2N/pdb
Entry: 6V2N supersedes: 6CU4

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

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.174
R-Value Work: 0.146
R-Value Observed: 0.146

wwPDB Validation 3D Report Full Report

Currently 6V2N does not have a validation slider image.

This is version 1.2 of the entry. See complete history.

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 Search on PubMed
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.

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: ats172@mail.usask.ca.

Macromolecule Content

Total Structure Weight: 59.53 kDa
Atom Count: 4,553
Modelled Residue Count: 518
Deposited Residue Count: 540
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphoenolpyruvate carboxykinase (ATP)	A	540	Escherichia coli	Mutation(s): 0 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22259
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.65 Å
R-Value Free: 0.174
R-Value Work: 0.146
R-Value Observed: 0.146
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.906	α = 90
b = 76.647	β = 96.38
c = 65.421	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Currently 6V2N does not have a validation slider image.

Entry History

Deposition Data

Released Date: 2019-12-25

Deposition Author(s):

This entry supersedes: 6CU4

Revision History (Full details and data files)

Version 1.0: 2019-12-25
Type: Initial release
Version 1.1: 2020-01-22
Changes: Database references
Version 1.2: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description