› 5k2m

X-ray diffraction
2.18Å resolution

Bifunctional LysX/ArgX from Thermococcus kodakarensis with LysW-gamma-AAA

Released:
DOI: 10.2210/pdb5k2m/pdb
PDB entry 5k2m coloured by chain, front view.
PDB entry 5k2m coloured by chain, side view.
PDB entry 5k2m coloured by chain, top view.
Source organism: Thermococcus kodakarensis KOD1
Primary publication:
Lysine Biosynthesis of Thermococcus kodakarensis with the Capacity to Function as an Ornithine Biosynthetic System.
Yoshida A, Tomita T, Atomi H, Kuzuyama T, Nishiyama M
J Biol Chem 291 21630-21643 (2016)
PMID: 27566549

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
hetero tetradecamer (preferred)
hetero hexamer
hetero octamer
Assembly name:
PDBe Complex ID:
PDB-CPX-177293 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
ATP-grasp domain-containing protein Chains: A, B, C, D, G, H, I, J
Molecule details ›
Chains: A, B, C, D, G, H, I, J
Length: 273 amino acids
Theoretical weight: 30.53 KDa
Source organism: Thermococcus kodakarensis KOD1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5JFW0 (Residues: 1-273; Coverage: 100%)
Gene name: TK0278
Sequence domains: RimK-like ATP-grasp domain
Structure domains:
Probable lysine biosynthesis protein Chains: E, F, K, L, M, N
Molecule details ›
Chains: E, F, K, L, M, N
Length: 53 amino acids
Theoretical weight: 5.98 KDa
Source organism: Thermococcus kodakarensis KOD1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5JFV9 (Residues: 1-53; Coverage: 100%)
Gene name: TK0279
Sequence domains: Alpha-aminoadipate carrier protein LysW-like, globular domain
Structure domains: Rubrerythrin, domain 2

Ligands and Environments

6 bound ligands:
Ligand ADP 8 x ADP
Ligand PO4 5 x PO4
Ligand MG 9 x MG
Ligand SO4 2 x SO4
Ligand ZN 2 x ZN
Ligand UN1 1 x UN1
1 modified residue:
Ligand R0K 6 x R0K

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: P21
Unit cell:
a: 76.15Å b: 135.099Å c: 136.977Å
α: 90° β: 97.49° γ: 90°
R-values:
R R work R free
0.182 0.18 0.22
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Biosynthesis of Oligopeptides Using ATP-Grasp Enzymes.
Ogasawara et al. (2017)
3 more

5 mentions without citation

Lysine Biosynthesis of Thermococcus kodakarensis with the Capacity to Function as an Ornithine Biosynthetic System.
Yoshida et al. (2016)
4 more