PDBsum entry 1ubh

Oxidoreductase

PDB id: 1ubh

Contents

Protein chains

267 a.a. *

534 a.a. *

Ligands

SF4 ×2

F3S

MPD ×11

FNE-CMO

Metals

_MG

Waters ×815

* Residue conservation analysis

PDB id:

1ubh

Name:

Oxidoreductase

Title:

Three-dimensional structure of the carbon monoxide complex of [nife]hydrogenase from desulufovibrio vulgaris miyazaki f

Structure:

Periplasmic [nife] hydrogenase small subunit. Chain: s. Synonym: small subunit of [nife]hydrogenase. Periplasmic [nife] hydrogenase large subunit. Chain: l. Fragment: residues 19-552. Synonym: large subunit of [nife]hydrogenase. Ec: 1.12.2.1

Source:

Desulfovibrio vulgaris str. 'Miyazaki f'. Organism_taxid: 883. Strain: miyazaki f. Strain: miyazaki f

Biol. unit:

Dimer (from PQS)

Resolution:

1.35Å R-factor: 0.131 R-free: 0.178

Authors:

H.Ogata,Y.Mizoguchi,N.Mizuno,K.Miki,S.Adachi,N.Yasuoka,T.Yagi, O.Yamauchi,S.Hirota,Y.Higuchi

Key ref:

H.Ogata et al. (2002). Structural studies of the carbon monoxide complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F: suggestion for the initial activation site for dihydrogen. J Am Chem Soc, 124, 11628-11635. PubMed id: 12296727 DOI: 10.1021/ja012645k

Date:

04-Apr-03 Release date: 29-Apr-03

Protein chain

P21853  (PHNS_DESVM) -  Periplasmic [NiFe] hydrogenase small subunit from Nitratidesulfovibrio vulgaris (strain DSM 19637 / Miyazaki F)

Seq: 317 a.a.

Struc: 267 a.a.

Protein chain

P21852  (PHNL_DESVM) -  Periplasmic [NiFe] hydrogenase large subunit from Nitratidesulfovibrio vulgaris (strain DSM 19637 / Miyazaki F)

Seq: 567 a.a.

Struc: 534 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chains S, L: 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: 10.1021/ja012645k

J Am Chem Soc 124:11628-11635 (2002)

PubMed id: 12296727

Structural studies of the carbon monoxide complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F: suggestion for the initial activation site for dihydrogen.

H.Ogata, Y.Mizoguchi, N.Mizuno, K.Miki, S.Adachi, N.Yasuoka, T.Yagi, O.Yamauchi, S.Hirota, Y.Higuchi.

ABSTRACT

The carbon monoxide complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F has been characterized by X-ray crystallography and absorption and resonance Raman spectroscopy. Nine crystal structures of the [NiFe]hydrogenase in the CO-bound and CO-liberated forms were determined at 1.2-1.4 A resolution. The exogenously added CO was assigned to be bound to the Ni atom at the Ni-Fe active site. The CO was not replaced with H(2) in the dark at 100 K, but was liberated by illumination with a strong white light. The Ni-C distances and Ni-C-O angles were about 1.77 A and 160 degrees, respectively, except for one case (1.72 A and 135 degrees ), in which an additional electron density peak between the CO and Sgamma(Cys546) was recognized. Distinct changes were observed in the electron density distribution of the Ni and Sgamma(Cys546) atoms between the CO-bound and CO-liberated structures for all the crystals tested. The novel structural features found near the Ni and Sgamma(Cys546) atoms suggest that these two atoms at the Ni-Fe active site play a role during the initial H(2)-binding process. Anaerobic addition of CO to dithionite-reduced [NiFe]hydrogenase led to a new absorption band at about 470 nm ( approximately 3000 M(-1)cm(-1)). Resonance Raman spectra (excitation at 476.5 nm) of the CO complex revealed CO-isotope-sensitive bands at 375/393 and 430 cm(-1) (368 and 413 cm(-1) for (13)C(18)O). The frequencies and relative intensities of the CO-related Raman bands indicated that the exogenous CO is bound to the Ni atom with a bent Ni-C-O structure in solution, in agreement with the refined structure determined by X-ray crystallography.