4Q5C

TvNiR in complex with sulfite, middle dose data set

Summary for 4Q5C

• Entry DOI: 10.2210/pdb4q5c/pdb
• Related: 4Q4U 4Q5B
• Descriptor: Eight-heme nitrite reductase, HEME C, SULFITE ION, ... (8 entities in total)
• Functional Keywords: 8 hemes c, oxidoreductase
• Biological source: Thioalkalivibrio nitratireducens
• Total number of polymer chains: 2
• Total formula weight: 129251.16

Authors

Lazarenko, V.A.,Polyakov, K.M.,Trofimov, A.A.,Popov, A.N.,Tikhonova, T.V.,Tikhonov, A.V.,Popov, V.O. (deposition date: 2014-04-16, release date: 2014-09-03, Last modification date: 2025-11-12)

Primary citation

Trofimov, A.A.,Polyakov, K.M.,Lazarenko, V.A.,Popov, A.N.,Tikhonova, T.V.,Tikhonov, A.V.,Popov, V.O.
Structural study of the X-ray-induced enzymatic reaction of octahaem cytochrome C nitrite reductase.
Acta Crystallogr.,Sect.D, 71:1087-1094, 2015

PubMed Abstract: Octahaem cytochrome c nitrite reductase from the bacterium Thioalkalivibrio nitratireducens catalyzes the reduction of nitrite to ammonium and of sulfite to sulfide. The reducing properties of X-ray radiation and the high quality of the enzyme crystals allow study of the catalytic reaction of cytochrome c nitrite reductase directly in a crystal of the enzyme, with the reaction being induced by X-rays. Series of diffraction data sets with increasing absorbed dose were collected from crystals of the free form of the enzyme and its complexes with nitrite and sulfite. The corresponding structures revealed gradual changes associated with the reduction of the catalytic haems by X-rays. In the case of the nitrite complex the conversion of the nitrite ions bound in the active sites to NO species was observed, which is the beginning of the catalytic reaction. For the free form, an increase in the distance between the oxygen ligand bound to the catalytic haem and the iron ion of the haem took place. In the case of the sulfite complex no enzymatic reaction was detected, but there were changes in the arrangement of the active-site water molecules that were presumably associated with a change in the protonation state of the sulfite ions.

PubMed: 25945574
DOI: 10.1107/S1399004715003053

Experimental method

X-RAY DIFFRACTION (1.62 Å)