› 3vpb

X-ray diffraction
1.8Å resolution

ArgX from Sulfolobus tokodaii complexed with LysW/Glu/ADP/Mg/Zn/Sulfate

Released:
DOI: 10.2210/pdb3vpb/pdb
PDB entry 3vpb coloured by chain, front view.
PDB entry 3vpb coloured by chain, side view.
PDB entry 3vpb coloured by chain, top view.
Source organism: Sulfurisphaera tokodaii str. 7
Primary publication:
Lysine and arginine biosyntheses mediated by a common carrier protein in Sulfolobus.
Ouchi T, Tomita T, Horie A, Yoshida A, Takahashi K, Nishida H, Lassak K, Taka H, Mineki R, Fujimura T, Kosono S, Nishiyama C, Masui R, Kuramitsu S, Albers SV, Kuzuyama T, Nishiyama M
Nat Chem Biol 9 277-83 (2013)
PMID: 23434852

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188816 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Glutamate--LysW ligase ArgX Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 282 amino acids
Theoretical weight: 31.57 KDa
Source organism: Sulfurisphaera tokodaii str. 7
Expression system: Escherichia coli
UniProt:
  • Canonical: Q970U6 (Residues: 1-282; Coverage: 100%)
Gene names: STK_15050, argE, argX
Sequence domains: RimK-like ATP-grasp domain
Structure domains:
Alpha-aminoadipate/glutamate carrier protein LysW Chains: E, F
Molecule details ›
Chains: E, F
Length: 56 amino acids
Theoretical weight: 6.11 KDa
Source organism: Sulfurisphaera tokodaii str. 7
Expression system: Escherichia coli
UniProt:
  • Canonical: Q976J8 (Residues: 1-56; Coverage: 100%)
Gene names: STK_01925, STS023, lysW
Sequence domains: Alpha-aminoadipate carrier protein LysW-like, globular domain
Structure domains: Rubrerythrin, domain 2

Ligands and Environments

5 bound ligands:
Ligand ADP 4 x ADP
Ligand GLU 4 x GLU
Ligand MG 4 x MG
Ligand ZN 4 x ZN
Ligand SO4 6 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NW12A
Spacegroup: P21
Unit cell:
a: 70.546Å b: 113.988Å c: 78.582Å
α: 90° β: 102.43° γ: 90°
R-values:
R R work R free
0.189 0.187 0.235
Expression system: Escherichia coli

Quick links

Citations

4 review citations

The N-Acetylglutamate Synthase Family: Structures, Function and Mechanisms.
Shi et al. (2015)
3 more

2 mentions without citation

Crystal Structure of the LysY·LysW Complex from Thermus thermophilus.
Shimizu et al. (2016)
1 more