ISDA: 5XVB

Deposition Date 2017-06-27

Release Date 2018-06-27

Last Version Date 2024-03-27

Entry Detail

PDB ID:

5XVB

Keywords:

OXIDOREDUCTASE

Title:

[NiFe]-hydrogenase (Hyb-type) from Citrobacter sp. S-77 in an H2-reduced condition

Biological Source:

Source Organism:

Citrobacter sp. S-77 (Taxon ID: 1080067)

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.84 Å

R-Value Free:

0.21

R-Value Work:

0.18

R-Value Observed:

0.18

Space Group:

P 1 21 1

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Macromolecular Entities

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:[NiFe]-hydrogenase 2 large subunit
Chain IDs:A (auth: L), C (auth: M)
Chain Length:567
Number of Molecules:2
Biological Source:Citrobacter sp. S-77

UniProt ID:A0A3B6UEP7 Pfam ID:PF00374

Structures with similar UniProt ID

Protein Blast

Polymer Type:polypeptide(L)
Molecule:[NiFe]-hydrogenase 2 small subunit
Chain IDs:B (auth: S), D (auth: T)
Chain Length:335
Number of Molecules:2
Biological Source:Citrobacter sp. S-77

UniProt ID:A0A3B6UEQ0 Pfam ID:PF01058, PF14720

Ligand Molecules

F3S

GOL

NFU

SF4

Primary Citation

Redox-dependent conformational changes of a proximal [4Fe-4S] cluster in Hyb-type [NiFe]-hydrogenase to protect the active site from O2.

Noor, N.D.M, Matsuura, H, Nishikawa, K, Tai, H, Hirota, S, Kim, J, Kang, J, Tateno, M, Yoon, K.S, Ogo, S, Kubota, S, Shomura, Y, Higuchi, Y.Show

Chem.Commun.(Camb.) 54 12385 12388 (2018)

PMID: 30328414 DOI: 10.1039/c8cc06261g

Abstact

Citrobacter sp. S-77 [NiFe]-hydrogenase harbors a standard [4Fe-4S] cluster proximal to the Ni-Fe active site. The presence of relocatable water molecules and a flexible aspartate enables the [4Fe-4S] to display redox-dependent conformational changes. These structural features are proposed to be the key aspects that protect the active site from O2 attack.

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Primary Citation of related structures