title: Genomic analysis reveals widespread occurrence of new classes of copper nitrite reductases.
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 beta-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 alpha, beta and gamma 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-A reach of the T1Cu centre of the T1Cu-T2Cu core.
authors: Molecular Biophysics Group, Science and Technology Facilities Council, Daresbury Laboratory, Warrington, Cheshire, UK.
authors: Mark J
authors: MJ
authors: Ellis
authors: J Günter
authors: JG
authors: Grossmann
authors: Robert R
authors: RR
authors: Eady
authors: S Samar
authors: SS
authors: Hasnain
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry* / Q000145:classification* / Q000235:genetics; D023281:Genomics; D006090:Gram-Negative Bacteria / Q000201:enzymology* / Q000235:genetics; D006418:Heme / Q000737:chemistry; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009572:Nitrite Reductases / Q000737:chemistry* / Q000145:classification* / Q000235:genetics; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D049920:Ralstonia pickettii / Q000201:enzymology; D020539:Sequence Analysis, Protein
chemical_list: D001426:Bacterial Proteins; D006418:Heme; D009572:Nitrite Reductases; C052695:nitrite reductase, copper-containing
references: Proc Natl Acad Sci U S A. 2007 Mar 13;104(11):4315-20
references: 17360521
references: J Clin Microbiol. 2003 May;41(5):2068-79
references: 12734250
references: Proteins. 2003 Jul 1;52(1):80-7
references: 12784371
references: Infect Control Hosp Epidemiol. 2006 Jun;27(6):642-4
references: 16755490
references: Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444-8
references: 3162770
references: Science. 1994 Apr 1;264(5155):86-90
references: 8140419
references: J Mol Biol. 2003 Apr 25;328(2):429-38
references: 12691751
references: J Mol Biol. 2006 Mar 17;357(1):151-62
references: 16414073
references: Methods Enzymol. 1990;183:63-98
references: 2156132
references: J Mol Biol. 1997 Aug 29;271(4):629-44
references: 9281430
references: Trends Genet. 2000 Jun;16(6):276-7
references: 10827456
references: Biochemistry. 1995 Sep 26;34(38):12107-17
references: 7547950
references: J Biol Chem. 2006 May 19;281(20):14503-13
references: 16554303
references: J Mol Biol. 2000 Jun 2;299(2):499-520
references: 10860755
references: Proc Natl Acad Sci U S A. 1997 Dec 23;94(26):14225-30
references: 9405594
references: J Mol Biol. 2002 Feb 1;315(5):1111-27
references: 11827480
references: J Biol Chem. 2001 Apr 13;276(15):11545-51
references: 11056172
references: Eur J Biochem. 2004 Jun;271(12):2361-9
references: 15182351
references: Nucleic Acids Res. 2007 Jul;35(Web Server issue):W407-10
references: 17517781
references: J Hosp Infect. 2006 Mar;62(3):278-84
references: 16337309
references: Structure. 2002 Jun;10(6):837-49
references: 12057198
references: Proteins. 1993 Dec;17(4):355-62
references: 8108378
references: Chem Rev. 2006 Jan;106(1):90-115
references: 16402772
references: Cell Mol Life Sci. 2005 Sep;62(18):2050-66
references: 16091847
references: Eur J Biochem. 1987 Oct 15;168(2):301-7
references: 3665926
references: FEBS Lett. 2004 Jul 2;569(1-3):7-12
references: 15225600
references: Acta Crystallogr D Biol Crystallogr. 2005 Sep;61(Pt 9):1190-8
references: 16131751
references: Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
references: 7984417
references: FEBS Lett. 2003 Oct 23;553(3):239-44
references: 14572631
references: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references: 9254694
references: J Biol Chem. 2002 Feb 1;277(5):3727-32
references: 11714714
references: Proc Natl Acad Sci U S A. 2005 Aug 23;102(34):12041-6
references: 16093314
references: J Mol Biol. 2002 Jul 5;320(2):263-75
references: 12079384