1UBK

Three-dimensional Structure of The Carbon Monoxide Complex of [NiFe]hydrogenase From Desulufovibrio vulgaris Miyazaki F

Summary for 1UBK

• Entry DOI: 10.2210/pdb1ubk/pdb
• Related: 1UBH 1UBJ 1UBL 1UBM 1UBO 1UBR 1UBT 1UBU
• Descriptor: Periplasmic [NiFe] hydrogenase Small subunit, Periplasmic [NiFe] hydrogenase Large subunit, IRON/SULFUR CLUSTER, ... (9 entities in total)
• Functional Keywords: high resolution crystal structure, [nife]hydrogenase, oxidoreductase, carbon monoxide complex
• Biological source: Desulfovibrio vulgaris str. 'Miyazaki F'; More
• Total number of polymer chains: 2
• Total formula weight: 90107.39

Authors

Ogata, H.,Mizoguchi, Y.,Mizuno, N.,Miki, K.,Adachi, S.,Yasuoka, N.,Yagi, T.,Yamauchi, O.,Hirota, S.,Higuchi, Y. (deposition date: 2003-04-04, release date: 2003-04-29, Last modification date: 2024-10-23)

Primary citation

Ogata, H.,Mizoguchi, Y.,Mizuno, N.,Miki, K.,Adachi, S.,Yasuoka, N.,Yagi, T.,Yamauchi, O.,Hirota, S.,Higuchi, Y.
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, 2002

PubMed 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.

PubMed: 12296727
DOI: 10.1021/ja012645k

Experimental method

X-RAY DIFFRACTION (1.18 Å)