PDBsum entry 4uql

Oxidoreductase

PDB id: 4uql

Contents

Protein chains

262 a.a.

544 a.a.

Ligands

SF4 ×4

F3S ×2

GOL ×11

GLY ×3

SOT

H2S

FCO-_NI ×2

Metals

_CL

_MG ×2

Waters ×1800

PDB id:

4uql

Name:

Oxidoreductase

Title:

High-resolution structure of a ni-a ni-sox mixture of the d. Fructosovorans nife-hydrogenase l122a mutant

Structure:

Hydrogenase (nife) small subunit hyda. Chain: a, b. Fragment: residues 50-314. Synonym: nife-hydrogenase small subunit. Engineered: yes. Nickel-dependent hydrogenase large subunit. Chain: q, r. Fragment: residues 2-549. Synonym: nife-hydrogenase large subunit.

Source:

Desulfovibrio fructosovorans. Organism_taxid: 878. Expressed in: desulfovibrio fructosovorans. Expression_system_taxid: 878. Expression_system_taxid: 878

Resolution:

1.22Å R-factor: 0.122 R-free: 0.152

Authors:

A.Volbeda,L.Martin,E.Barbier,O.Gutierrez-Sanz,A.L.Delacey, P.P.Liebgott,S.Dementin,M.Rousset,J.C.Fontecilla-Camps

Key ref:

A.Volbeda et al. (2015). Crystallographic studies of [NiFe]-hydrogenase mutants: towards consensus structures for the elusive unready oxidized states. J Biol Inorg Chem, 20, 11-22. PubMed id: 25315838 DOI: 10.1007/s00775-014-1203-9

Date:

24-Jun-14 Release date: 29-Oct-14

Protein chains

P18187  (PHNS_SOLFR) -  Periplasmic [NiFe] hydrogenase small subunit from Solidesulfovibrio fructosivorans

Seq: 314 a.a.

Struc: 262 a.a.

Protein chains

P18188  (PHNL_SOLFR) -  Periplasmic [NiFe] hydrogenase large subunit from Solidesulfovibrio fructosivorans

Seq: 564 a.a.

Struc: 545 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, Q, R: E.C.1.12.2.1 - cytochrome-c3 hydrogenase.
• Reaction: 2 Fe(III)-[cytochrome c3] + H2 = 2 Fe(II)-[cytochrome c3] + 2 H⁺
• Cofactor: Iron-sulfur; Ni(2+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key reference

DOI no: 10.1007/s00775-014-1203-9

J Biol Inorg Chem 20:11-22 (2015)

PubMed id: 25315838

Crystallographic studies of [NiFe]-hydrogenase mutants: towards consensus structures for the elusive unready oxidized states.

A.Volbeda, L.Martin, E.Barbier, O.Gutiérrez-Sanz, A.L.De Lacey, P.P.Liebgott, S.Dementin, M.Rousset, J.C.Fontecilla-Camps.

ABSTRACT

Catalytically inactive oxidized O2-sensitive [NiFe]-hydrogenases are characterized by a mixture of the paramagnetic Ni-A and Ni-B states. Upon O2 exposure, enzymes in a partially reduced state preferentially form the unready Ni-A state. Because partial O2 reduction should generate a peroxide intermediate, this species was previously assigned to the elongated Ni-Fe bridging electron density observed for preparations of [NiFe]-hydrogenases known to contain the Ni-A state. However, this proposition has been challenged based on the stability of this state to UV light exposure and the possibility of generating it anaerobically under either chemical or electrochemical oxidizing conditions. Consequently, we have considered alternative structures for the Ni-A species including oxidation of thiolate ligands to either sulfenate or sulfenic acid. Here, we report both new and revised [NiFe]-hydrogenases structures and conclude, taking into account corresponding characterizations by Fourier transform infrared spectroscopy (FTIR), that the Ni-A species contains oxidized cysteine and bridging hydroxide ligands instead of the peroxide ligand we proposed earlier. Our analysis was rendered difficult by the typical formation of mixtures of unready oxidized states that, furthermore, can be reduced by X-ray induced photoelectrons. The present study could be carried out thanks to the use of Desulfovibrio fructosovorans [NiFe]-hydrogenase mutants with special properties. In addition to the Ni-A state, crystallographic results are also reported for two diamagnetic unready states, allowing the proposal of a revised oxidized inactive Ni-SU model and a new structure characterized by a persulfide ion that is assigned to an Ni-'Sox' species.