› 7utd

Electron Microscopy
2.19Å resolution

The 2.19-angstrom CryoEM structure of the [NiFe]-hydrogenase Huc from Mycobacterium smegmatis - Complex minus stalk

Released:
DOI: 10.2210/pdb7utd/pdb
PDB entry 7utd coloured by chain, front view.
PDB entry 7utd coloured by chain, side view.
PDB entry 7utd coloured by chain, top view.
Source organism: Mycolicibacterium smegmatis MC2 155
Primary publication:
Structural basis for bacterial energy extraction from atmospheric hydrogen.
Grinter R, Kropp A, Venugopal H, Senger M, Badley J, Cabotaje PR, Jia R, Duan Z, Huang P, Stripp ST, Barlow CK, Belousoff M, Shafaat HS, Cook GM, Schittenhelm RB, Vincent KA, Khalid S, Berggren G, Greening C
OpenAccess logo Nature (2023)
PMID: 36890228
Related structures: EMD-26767

Function and Biology Details

Reaction catalysed: 
H(2) + A = AH(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero icosamer (preferred)
PDBe Complex ID:
PDB-CPX-222100 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Hydrogenase-2, large subunit Chains: A, C, E, G, I, K, M, O
Molecule details ›
Chains: A, C, E, G, I, K, M, O
Length: 513 amino acids
Theoretical weight: 57.22 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QUM7 (Residues: 4-516; Coverage: 96%)
Gene names: MSMEG_2263, hybC
Sequence domains: Nickel-dependent hydrogenase
Hydrogenase-2, small subunit Chains: B, D, F, H, J, L, N, P
Molecule details ›
Chains: B, D, F, H, J, L, N, P
Length: 369 amino acids
Theoretical weight: 39.66 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QUM6 (Residues: 2-323; Coverage: 100%)
Gene names: MSMEG_2262, hybA
Sequence domains:
DUF1641 domain-containing protein Chains: Q, R, S, T
Molecule details ›
Chains: Q, R, S, T
Length: 60 amino acids
Theoretical weight: 6.42 KDa
Source organism: Mycolicibacterium smegmatis MC2 155
UniProt:
  • Canonical: A0QUM5 (Residues: 20-79; Coverage: 32%)
Gene name: MSMEG_2261

Ligands and Environments

5 bound ligands:
Ligand 3NI 8 x 3NI
Ligand FCO 8 x FCO
Ligand MG 8 x MG
Ligand MQ9 8 x MQ9
Ligand F3S 24 x F3S
1 modified residue:
Ligand DHI 8 x DHI

Experiments and Validation Details

Entry percentile scores
Resolution: 2.19Å
Relevant EMDB volumes: EMD-26767

Quick links

Citations

6 review citations

Outer-sphere effects on the O2 sensitivity, catalytic bias and catalytic reversibility of hydrogenases.
Fasano et al. (2024)
5 more

1 mention without citation

Protein target highlights in CASP15: Analysis of models by structure providers.
Alexander et al. (2023)