3SCE: Structure Of The Thioalkalivibrio Nitratireducens Cytochrome C Nitrite Reductase With A Covalent Bond Between The Ce1 Atom Of Tyr303 And The Cg Atom Of Gln360 (Tvnirb)

Citation:
Abstract
Octahaem cytochrome c nitrite reductase from Thioalkalivibrio nitratireducens (TvNiR), like the previously characterized pentahaem nitrite reductases (NrfAs), catalyzes the six-electron reductions of nitrite to ammonia and of sulfite to sulfide. The active site of both TvNiR and NrfAs is formed by the lysine-coordinated haem and His, Tyr and Arg residues. The distinguishing structural feature of TvNiR is the presence of a covalent bond between the CE2 atom of the catalytic Tyr303 and the S atom of Cys305, which might be responsible for the higher nitrite reductase activity of TvNiR compared with NrfAs. In the present study, a new modified form of the enzyme (TvNiRb) that contains an additional covalent bond between Tyr303 CE1 and Gln360 CG is reported. Structures of TvNiRb in complexes with phosphate (1.45 A resolution) and sulfite (1.8 A resolution), the structure of TvNiR in a complex with nitrite (1.83 A resolution) and several additional structures were determined. The formation of the second covalent bond by Tyr303 leads to a decrease in both the nitrite and sulfite reductase activities of the enzyme. Tyr303 is located at the exit from the putative proton-transport channel to the active site, which is absent in NrfAs. This is an additional argument in favour of the involvement of Tyr303 as a proton donor in catalysis. The changes in the activity of cytochrome c nitrite reductases owing to the formation of Tyr-Cys and Tyr-Gln bonds may be associated with changes in the pK(a) value of the catalytic tyrosine.
PDB ID: 3SCEDownload
MMDB ID: 91416
PDB Deposition Date: 2011/6/7
Updated in MMDB: 2011/07
Experimental Method:
x-ray diffraction
Resolution: 1.45  Å
Source Organism:
Similar Structures:
Biological Unit for 3SCE: hexameric; determined by author and by software (PISA)
Molecular Components in 3SCE
Label Count Molecule
Proteins (6 molecules)
6
Eight-heme Nitrite Reductase
Molecule annotation
Chemicals (136 molecules)
1
48
2
7
3
12
4
48
5
15
6
6
* Click molecule labels to explore molecular sequence information.

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