› 5aun

X-ray diffraction
1.63Å resolution

Crystal structure of the HypAB-Ni complex

Released:
DOI: 10.2210/pdb5aun/pdb
PDB entry 5aun coloured by chain, front view.
PDB entry 5aun coloured by chain, side view.
PDB entry 5aun coloured by chain, top view.
Source organism: Thermococcus kodakarensis KOD1
Primary publication:
Structural basis of a Ni acquisition cycle for [NiFe] hydrogenase by Ni-metallochaperone HypA and its enhancer.
Watanabe S, Kawashima T, Nishitani Y, Kanai T, Wada T, Inaba K, Atomi H, Imanaka T, Miki K
Proc Natl Acad Sci U S A 112 7701-6 (2015)
PMID: 26056269

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-177311 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Hydrogenase maturation factor HypA Chain: A
Molecule details ›
Chain: A
Length: 139 amino acids
Theoretical weight: 15.71 KDa
Source organism: Thermococcus kodakarensis KOD1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5JIH3 (Residues: 1-139; Coverage: 100%)
Gene names: TK2008, hypA
Sequence domains: Hydrogenase/urease nickel incorporation, metallochaperone, hypA
Structure domains: hypothetical protein PF0899 fold
Iron-sulfur cluster carrier protein Chain: B
Molecule details ›
Chain: B
Length: 248 amino acids
Theoretical weight: 27.62 KDa
Source organism: Thermococcus kodakarensis KOD1
Expression system: Escherichia coli
UniProt:
  • Canonical: Q5JIH4 (Residues: 1-248; Coverage: 100%)
Gene name: TK2007
Sequence domains: NUBPL iron-transfer P-loop NTPase
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

7 bound ligands:
Ligand ZN 1 x ZN
Ligand NI 1 x NI
Ligand URE 3 x URE
Ligand CL 1 x CL
Ligand GOL 2 x GOL
Ligand ADP 1 x ADP
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-1A
Spacegroup: P21212
Unit cell:
a: 74.72Å b: 82.744Å c: 65.128Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.182 0.18 0.213
Expression system: Escherichia coli

Quick links

Citations

6 review citations

Metallochaperones and metalloregulation in bacteria.
Capdevila et al. (2017)
5 more

4 mentions without citation

Structural basis of a Ni acquisition cycle for [NiFe] hydrogenase by Ni-metallochaperone HypA and its enhancer.
Watanabe et al. (2015)
3 more