› 5od2

X-ray diffraction
1.98Å resolution

Crystal structure of ADP-dependent glucokinase from Methanocaldococcus jannaschii

Released:
DOI: 10.2210/pdb5od2/pdb
PDB entry 5od2 coloured by chain, front view.
PDB entry 5od2 coloured by chain, side view.
PDB entry 5od2 coloured by chain, top view.
Source organism: Methanocaldococcus jannaschii DSM 2661
Primary publication:
Crystal structure of ADP-dependent glucokinase from Methanocaldococcus jannaschii in complex with 5-iodotubercidin reveals phosphoryl transfer mechanism.
Tokarz P, Wiśniewska M, Kamiński MM, Dubin G, Grudnik P
Protein Sci 27 790-797 (2018)
PMID: 29352744

Function and Biology Details

Reactions catalysed: 
ADP + D-fructose 6-phosphate = AMP + D-fructose 1,6-bisphosphate
ADP + D-glucosamine = AMP + D-glucosamine 6-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-176732 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Bifunctional ADP-specific glucokinase/phosphofructokinase Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 458 amino acids
Theoretical weight: 53.01 KDa
Source organism: Methanocaldococcus jannaschii DSM 2661
Expression system: Escherichia coli
UniProt:
  • Canonical: Q58999 (Residues: 4-461; Coverage: 99%)
Gene names: MJ1604, glkA, pfkC
Sequence domains: ADP-specific Phosphofructokinase/Glucokinase conserved region
Structure domains:

Ligands and Environments

4 bound ligands:
Ligand GLC 3 x GLC
Ligand 5ID 3 x 5ID
Ligand MG 3 x MG
Ligand PO4 3 x PO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P31
Unit cell:
a: 154.565Å b: 154.565Å c: 50.483Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.188 0.186 0.224
Expression system: Escherichia coli

Quick links

Citations

3 citation in other articles

Structural basis for ADP-dependent glucokinase inhibition by 8-bromo-substituted adenosine nucleotide.
Grudnik et al. (2018)
2 more

2 mentions without citation

Crystal structure of ADP-dependent glucokinase from Methanocaldococcus jannaschii in complex with 5-iodotubercidin reveals phosphoryl transfer mechanism.
Tokarz et al. (2018)
1 more