Genomic analysis reveals widespread occurrence of new classes of copper nitrite reductases
- 22 August 2007
- journal article
- Published by Springer Science and Business Media LLC in JBIC Journal of Biological Inorganic Chemistry
- Vol. 12 (8), 1119-1127
- https://doi.org/10.1007/s00775-007-0282-2
Abstract
Recently, the structure of a Cu-containing nitrite reductase (NiR) from Hyphomicrobium denitrificans (HdNiR) has been reported, establishing the existence of a new family of Cu-NiR where an additional type 1 Cu (T1Cu) containing cupredoxin domain is located at the N-terminus (Nojiri et al. in Proc. Natl. Acad. Sci. USA 104:4315–4320, 2007). HdNiR retains the well-characterised coupled T1Cu–type 2 Cu (T2Cu) core, where the T2Cu catalytic site is also built utilising ligands from neighbouring monomers. We have undertaken a genome analysis and found the wide occurrence of these NiRs, with members clustering in two groups, one showing an amino acid sequence similarity of around 80% with HdNiR, and a second group, including the NiR from the extremophile Acidothermus cellulolyticus, clustering around 50% similarity to HdNiR. This is reminiscent of the difference observed between the blue (Alcaligenes xylosoxidans) and green (Achromobacter cycloclastes and Alcaligenes faecalis) NiRs which have been extensively studied and may indicate that these also form two distinct subclasses of the new family. Genome analysis also showed the presence of Cu-NiRs with a C-terminal extension of 160–190 residues containing a class I cytochrome c domain with a characteristic β-sheet extension. Currently no structural information exists for any member of this family. Genome analysis suggests the widespread occurrence of these novel NiRs with representatives in the α, β and γ subclasses of the Proteobacteria and in two species of the fungus Aspergillus. We selected the enzyme from Ralstonia pickettii for comparative modelling and produced a plausible structure highlighting an electron transfer mode in which the cytochrome c haem at the C-terminus can come within 16-Å reach of the T1Cu centre of the T1Cu–T2Cu core.Keywords
This publication has 35 references indexed in Scilit:
- ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteinsNucleic Acids Research, 2007
- Structure and function of a hexameric copper-containing nitrite reductaseProceedings of the National Academy of Sciences of the United States of America, 2007
- The 1.6Å X-ray Structure of the Unusual c-type Cytochrome, Cytochrome cL, from the Methylotrophic Bacterium Methylobacterium extorquensJournal of Molecular Biology, 2006
- Crystal Structures of the Met148Leu and Ser86Asp Mutants of Rusticyanin from Thiobacillus ferrooxidans: Insights into the Structural Relationship with the Cupredoxins and the Multi Copper ProteinsJournal of Molecular Biology, 2002
- Structure at 1.9 Å Resolution of a Quinohemoprotein Alcohol Dehydrogenase from Pseudomonas putida HK5Structure, 2002
- Crystal Structure of Quinohemoprotein Alcohol Dehydrogenase from Comamonas testosteroniPublished by Elsevier BV ,2002
- Crystal structure of the soluble domain of the major anaerobically induced outer membrane protein (AniA) from pathogenic Neisseria: a new class of copper-containing nitrite reductasesJournal of Molecular Biology, 2002
- Electron Transfer and Binding of the c-Type Cytochrome TorC to the Trimethylamine N-Oxide Reductase in Escherichia coliJournal of Biological Chemistry, 2001
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997
- CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choiceNucleic Acids Research, 1994