› 4gnp

X-ray diffraction
1.74Å resolution

Structure of rat cytosolic PEPCK Ld_3g in complex with PEP and GDP

Released:
DOI: 10.2210/pdb4gnp/pdb
PDB entry 4gnp coloured by chain, front view.
PDB entry 4gnp coloured by chain, side view.
PDB entry 4gnp coloured by chain, top view.
Source organism: Rattus norvegicus
Primary publication:
The Ω-loop lid domain of phosphoenolpyruvate carboxykinase is essential for catalytic function.
Johnson TA, Holyoak T
Biochemistry 51 9547-59 (2012)
PMID: 23127136

Function and Biology Details

Reaction catalysed: 
GTP + oxaloacetate = GDP + phosphoenolpyruvate + CO(2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
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] Chain: A
Molecule details ›
Chain: A
Length: 614 amino acids
Theoretical weight: 68.6 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P07379 (Residues: 1-463, 475-622; Coverage: 98%)
Gene name: Pck1
Sequence domains:
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand GDP 1 x GDP
Ligand MN 2 x MN
Ligand PEP 1 x PEP
Ligand NA 1 x NA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL7-1
Spacegroup: P212121
Unit cell:
a: 60.875Å b: 84.612Å c: 118.842Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.187 0.185 0.24
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

14 citation in other articles

The activating oxydianion binding domain for enzyme-catalyzed proton transfer, hydride transfer, and decarboxylation: specificity and enzyme architecture.
Reyes et al. (2015)
13 more

2 mentions without citation

The Ω-loop lid domain of phosphoenolpyruvate carboxykinase is essential for catalytic function.
Johnson et al. (2012)
1 more