› 6ehs

X-ray diffraction
1.5Å resolution

E. coli Hydrogenase-2 chemically reduced structure

Released:
DOI: 10.2210/pdb6ehs/pdb
PDB entry 6ehs coloured by chain, front view.
PDB entry 6ehs coloured by chain, side view.
PDB entry 6ehs coloured by chain, top view.
Source organism: Escherichia coli K-12
Primary publication:
The structure of hydrogenase-2 from Escherichia coli: implications for H2-driven proton pumping.
Beaton SE, Evans RM, Finney AJ, Lamont CM, Armstrong FA, Sargent F, Carr SB
Biochem J 475 1353-1370 (2018)
PMID: 29555844

Function and Biology Details

Reaction catalysed: 
H(2) + A = AH(2)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-110522 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
hydrogenase (acceptor) Chains: S, T
Molecule details ›
Chains: S, T
Length: 300 amino acids
Theoretical weight: 32.63 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: B7LGE4 (Residues: 38-330; Coverage: 79%)
Gene names: EC55989_3414, hybO
Sequence domains:
Structure domains:
Hydrogenase-2 large chain Chains: L, M
Molecule details ›
Chains: L, M
Length: 552 amino acids
Theoretical weight: 61.05 KDa
Source organism: Escherichia coli K-12
Expression system: Escherichia coli
UniProt:
  • Canonical: P0ACE1 (Residues: 1-552; Coverage: 97%)
Gene names: ECs3879, Z4348, hybC
Sequence domains: Nickel-dependent hydrogenase
Structure domains: Cytochrome-c3 Hydrogenase, chain B

Ligands and Environments

6 bound ligands:
Ligand SF4 4 x SF4
Ligand F3S 2 x F3S
Ligand FCO 2 x FCO
Ligand NI 2 x NI
Ligand MG 2 x MG
Ligand DTN 4 x DTN
1 modified residue:
Ligand CSO 2 x CSO

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I03
Spacegroup: P212121
Unit cell:
a: 99.885Å b: 100.065Å c: 168.801Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.126 0.124 0.163
Expression system: Escherichia coli

Quick links

Citations

5 review citations

Molecular Hydrogen Metabolism: a Widespread Trait of Pathogenic Bacteria and Protists.
Benoit et al. (2020)
4 more

1 mention without citation

The structure of hydrogenase-2 from Escherichia coli: implications for H2-driven proton pumping.
Beaton et al. (2018)