› 2rk8

X-ray diffraction
2Å resolution

The Structure of rat cytosolic PEPCK in complex with phosphonoformate

Released:
DOI: 10.2210/pdb2rk8/pdb
PDB entry 2rk8 coloured by chain, front view.
PDB entry 2rk8 coloured by chain, side view.
PDB entry 2rk8 coloured by chain, top view.
Source organism: Rattus norvegicus
Primary publication:
Differential inhibition of cytosolic PEPCK by substrate analogues. Kinetic and structural characterization of inhibitor recognition.
Stiffin RM, Sullivan SM, Carlson GM, Holyoak T
Biochemistry 47 2099-109 (2008)
PMID: 18197707

Function and Biology Details

Reaction catalysed: 
GTP + oxaloacetate = GDP + phosphoenolpyruvate + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-139574 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phosphoenolpyruvate carboxykinase, cytosolic [GTP] Chains: A, B
Molecule details ›
Chains: A, B
Length: 624 amino acids
Theoretical weight: 69.64 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P07379 (Residues: 1-622; Coverage: 100%)
Gene name: Pck1
Sequence domains:
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand MN 2 x MN
Ligand NA 2 x NA
Ligand PPF 2 x PPF
Ligand FMT 2 x FMT
Ligand PEG 1 x PEG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RUH3R
Spacegroup: P21
Unit cell:
a: 62.251Å b: 119.47Å c: 86.87Å
α: 90° β: 107.06° γ: 90°
R-values:
R R work R free
0.198 0.195 0.249
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 review citations

The mitochondrial isoform of phosphoenolpyruvate carboxykinase (PEPCK-M) and glucose homeostasis: has it been overlooked?
Stark et al. (2014)
1 more

1 mention without citation

Computational evaluation of natural compounds as potential inhibitors of human PEPCK-M: an alternative for lung cancer therapy.
Baptista et al. (2019)