ISDA: 6G94

Deposition Date 2018-04-10

Release Date 2018-06-13

Last Version Date 2024-01-17

Entry Detail

PDB ID:

6G94

Keywords:

OXIDOREDUCTASE

Title:

Structure of E. coli hydrogenase-1 C19G variant in complex with cytochrome b

Biological Source:

Source Organism:

Escherichia coli K-12 (Taxon ID: 83333)

Host Organism:

Escherichia coli

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

2.50 Å

R-Value Free:

0.25

R-Value Work:

0.22

R-Value Observed:

0.22

Space Group:

P 21 21 21

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Probable Ni/Fe-hydrogenase 1 B-type cytochrome subunit
Gene (Uniprot):hyaC
Chain IDs:I (auth: A), J (auth: B)
Chain Length:235
Number of Molecules:2
Biological Source:Escherichia coli K-12

UniProt ID:P0AAM1 Pfam ID:PF01292

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Hydrogenase-1 large chain
Gene (Uniprot):hyaB
Chain IDs:B (auth: L), D (auth: M), F (auth: J), H (auth: K)
Chain Length:582
Number of Molecules:4
Biological Source:Escherichia coli (strain K12)

UniProt ID:P0ACD8 Pfam ID:PF00374 EC:1.12.99.6

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:Hydrogenase-1 small chain
Gene (Uniprot):hyaA
Chain IDs:A (auth: S), C (auth: T), E (auth: Q), G (auth: R)
Chain Length:335
Number of Molecules:4
Biological Source:Escherichia coli K-12

UniProt ID:P69739 Pfam ID:PF01058, PF14720 EC:1.12.99.6

Ligand Molecules

ER2

F3S

FCO

HEM

SF4

Primary Citation

X-ray structural, functional and computational studies of the O2-sensitive E. coli hydrogenase-1 C19G variant reveal an unusual [4Fe-4S] cluster.

Volbeda, A, Mouesca, J.M, Darnault, C, Roessler, M.M, Parkin, A, Armstrong, F.A, Fontecilla-Camps, J.C, Volbeda, A, Darnault, C, Parkin, A, Sargent, F, Armstrong, F.A, Fontecilla-Camps, J.C, Evans, R.M, Parkin, A, Roessler, M.M, Murphy, B.J, Adamson, H, Lukey, M.J, Sargent, F, Volbeda, A, Fontecilla-Camps, J.C, Armstrong, F.A, Volbeda, A, Amara, P, Darnault, C, Mouesca, J.M, Parkin, A, Roessler, M.M, Armstrong, F.A, Fontecilla-Camps, J.C.Show

Chem. Commun. (Camb.) 54 7175 7178 (2018)

PMID: 29888350 DOI: 10.1039/c8cc02896f

Abstact

The crystal structure of the Escherichia coli O2-sensitive C19G [NiFe]-hydrogenase-1 variant shows that the mutation results in a novel FeS cluster, proximal to the Ni-Fe active site. While the proximal cluster of the native O2-tolerant enzyme can transfer two electrons to that site, EPR spectroscopy shows that the modified cluster can transfer only one electron, this shortfall coinciding with O2 sensitivity. Computational studies on electron transfer help to explain how the structural and redox properties of the novel FeS cluster modulate the observed phenotype.

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Primary Citation of related structures