ID NIR_ALCFA Reviewed; 376 AA. AC P38501; DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot. DT 01-OCT-1994, sequence version 1. DT 08-NOV-2023, entry version 126. DE RecName: Full=Copper-containing nitrite reductase; DE EC=1.7.2.1; DE AltName: Full=Cu-NIR; DE Flags: Precursor; GN Name=nirK; Synonyms=nir; OS Alcaligenes faecalis. OC Bacteria; Pseudomonadota; Betaproteobacteria; Burkholderiales; OC Alcaligenaceae; Alcaligenes. OX NCBI_TaxID=511; RN [1] RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 34-48 AND 192-240, RP AND PYROGLUTAMATE FORMATION AT GLN-34. RC STRAIN=S-6; RX PubMed=8515232; DOI=10.1099/00221287-139-4-725; RA Nishiyama M., Suzuki J., Kukimoto M., Ohnuki T., Horinouchi S., Beppu T.; RT "Cloning and characterization of a nitrite reductase gene from Alcaligenes RT faecalis and its expression in Escherichia coli."; RL J. Gen. Microbiol. 139:725-733(1993). RN [2] RP X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS), AND MUTAGENESIS. RC STRAIN=S-6; RX PubMed=8172899; DOI=10.1021/bi00183a030; RA Kukimoto M., Nishiyama M., Murphy M.E.P., Turley S., Adman E.T., RA Horinouchi S., Beppu T.; RT "X-ray structure and site-directed mutagenesis of a nitrite reductase from RT Alcaligenes faecalis S-6: roles of two copper atoms in nitrite reduction."; RL Biochemistry 33:5246-5252(1994). RN [3] RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS). RX PubMed=7547950; DOI=10.1021/bi00038a003; RA Murphy M.E., Turley S., Kukimoto M., Nishiyama M., Horinouchi S., RA Sasaki H., Tanokura M., Adman E.T.; RT "Structure of Alcaligenes faecalis nitrite reductase and a copper site RT mutant, M150E, that contains zinc."; RL Biochemistry 34:12107-12117(1995). RN [4] RP X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS). RX PubMed=9353305; DOI=10.1074/jbc.272.45.28455; RA Murphy M.E., Turley S., Adman E.T.; RT "Structure of nitrite bound to copper-containing nitrite reductase from RT Alcaligenes faecalis. Mechanistic implications."; RL J. Biol. Chem. 272:28455-28460(1997). CC -!- CATALYTIC ACTIVITY: CC Reaction=Fe(III)-[cytochrome c] + H2O + nitric oxide = Fe(II)- CC [cytochrome c] + 2 H(+) + nitrite; Xref=Rhea:RHEA:15233, Rhea:RHEA- CC COMP:10350, Rhea:RHEA-COMP:14399, ChEBI:CHEBI:15377, CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16301, ChEBI:CHEBI:16480, CC ChEBI:CHEBI:29033, ChEBI:CHEBI:29034; EC=1.7.2.1; CC -!- COFACTOR: CC Name=Cu(2+); Xref=ChEBI:CHEBI:29036; Evidence={ECO:0000250}; CC Note=Binds 1 Cu(2+) ion. The Cu(2+) ion is held by residues from each CC of 2 monomers of the trimer. Nitrite is bound to the Cu(2+) ion site. CC Pseudoazurin is the physiological electron donor for the Cu-NIR in CC vitro. {ECO:0000250}; CC -!- COFACTOR: CC Name=Cu(+); Xref=ChEBI:CHEBI:49552; Evidence={ECO:0000250}; CC Note=Binds 1 Cu(+) ion. The Cu(+) ion is bound within a single monomer. CC {ECO:0000250}; CC -!- COFACTOR: CC Name=FAD; Xref=ChEBI:CHEBI:57692; Evidence={ECO:0000250}; CC -!- PATHWAY: Nitrogen metabolism; nitrate reduction (denitrification); CC dinitrogen from nitrate: step 2/4. CC -!- SUBUNIT: Homotrimer. CC -!- SUBCELLULAR LOCATION: Periplasm. CC -!- INDUCTION: Under anaerobic growth conditions and by nitrite. CC -!- DOMAIN: The type I copper site in NIR plays a crucial role for electron CC transfer from pseudoazurin to the type II copper site of NIR, which CC comprises the catalytic center of NIR for the reduction of nitrite. CC -!- PTM: Predicted to be exported by the Tat system. The position of the CC signal peptide cleavage has been experimentally proven. CC -!- SIMILARITY: Belongs to the multicopper oxidase family. {ECO:0000305}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; D13155; BAA02440.1; -; Genomic_DNA. DR PIR; I39582; I39582. DR PDB; 1AQ8; X-ray; 2.00 A; A/B/C=34-376. DR PDB; 1AS6; X-ray; 1.80 A; A/B/C=34-376. DR PDB; 1AS7; X-ray; 2.00 A; A/B/C=34-376. DR PDB; 1AS8; X-ray; 1.85 A; A/B/C=34-376. DR PDB; 1ET5; X-ray; 1.90 A; A=40-376. DR PDB; 1ET7; X-ray; 1.70 A; A=40-376. DR PDB; 1ET8; X-ray; 1.80 A; A=40-376. DR PDB; 1J9Q; X-ray; 1.65 A; A/B/C=40-376. DR PDB; 1J9R; X-ray; 2.00 A; A/B/C=40-376. DR PDB; 1J9S; X-ray; 1.90 A; A/B/C=40-376. DR PDB; 1J9T; X-ray; 1.95 A; A/B/C=40-376. DR PDB; 1L9O; X-ray; 1.70 A; A/B/C=40-376. DR PDB; 1L9P; X-ray; 1.75 A; A/B/C=40-376. DR PDB; 1L9Q; X-ray; 1.70 A; A/B/C=40-376. DR PDB; 1L9R; X-ray; 1.78 A; A/B/C=40-376. DR PDB; 1L9S; X-ray; 1.78 A; A/B/C=40-376. DR PDB; 1L9T; X-ray; 1.75 A; A/B/C=40-376. DR PDB; 1NPJ; X-ray; 1.90 A; A/B/C=34-376. DR PDB; 1NPN; X-ray; 1.80 A; A/B/C=34-376. DR PDB; 1NTD; X-ray; 2.30 A; A=34-376. DR PDB; 1SJM; X-ray; 1.40 A; A/B/C=40-376. DR PDB; 1SNR; X-ray; 1.31 A; A/B/C=40-376. DR PDB; 1ZDQ; X-ray; 1.80 A; A/B/C=40-375. DR PDB; 1ZDS; X-ray; 1.55 A; A/B/C=40-375. DR PDB; 2AFN; X-ray; 2.00 A; A/B/C=34-376. DR PDB; 2B08; X-ray; 1.90 A; A/B/C=37-376. DR PDB; 2E86; X-ray; 1.50 A; A/B/C=40-376. DR PDB; 2FJS; X-ray; 1.85 A; A/B/C=40-376. DR PDB; 2P80; NMR; -; A/B/C=40-376. DR PDB; 2PP7; X-ray; 1.65 A; A/B/C=40-376. DR PDB; 2PP8; X-ray; 1.50 A; A/B/C=40-376. DR PDB; 2PP9; X-ray; 1.80 A; A/B/C=40-376. DR PDB; 2PPA; X-ray; 1.69 A; A/B/C=40-376. DR PDB; 2PPC; X-ray; 1.58 A; A/B/C=40-376. DR PDB; 2PPD; X-ray; 1.80 A; A/B/C=34-376. DR PDB; 2PPE; X-ray; 1.75 A; A/B/C=34-376. DR PDB; 2PPF; X-ray; 1.65 A; A/B/C=40-376. DR PDB; 3H4F; X-ray; 2.10 A; A/B/C=40-375. DR PDB; 3H4H; X-ray; 1.60 A; A/B/C=41-375. DR PDB; 3H56; X-ray; 1.50 A; A=40-375. DR PDB; 4YSC; X-ray; 2.03 A; A/B/C=40-376. DR PDB; 4YSE; X-ray; 1.20 A; A/B/C=40-376. DR PDB; 5D4H; X-ray; 1.30 A; A/B/C=40-376. DR PDB; 5D4I; X-ray; 1.60 A; A/B/C=40-376. DR PDB; 5D4J; X-ray; 2.00 A; A/B/C=40-376. DR PDB; 5F7A; X-ray; 1.54 A; A/B/C=40-376. DR PDB; 5F7B; X-ray; 1.56 A; A/B/C=40-376. DR PDBsum; 1AQ8; -. DR PDBsum; 1AS6; -. DR PDBsum; 1AS7; -. DR PDBsum; 1AS8; -. DR PDBsum; 1ET5; -. DR PDBsum; 1ET7; -. DR PDBsum; 1ET8; -. DR PDBsum; 1J9Q; -. DR PDBsum; 1J9R; -. DR PDBsum; 1J9S; -. DR PDBsum; 1J9T; -. DR PDBsum; 1L9O; -. DR PDBsum; 1L9P; -. DR PDBsum; 1L9Q; -. DR PDBsum; 1L9R; -. DR PDBsum; 1L9S; -. DR PDBsum; 1L9T; -. DR PDBsum; 1NPJ; -. DR PDBsum; 1NPN; -. DR PDBsum; 1NTD; -. DR PDBsum; 1SJM; -. DR PDBsum; 1SNR; -. DR PDBsum; 1ZDQ; -. DR PDBsum; 1ZDS; -. DR PDBsum; 2AFN; -. DR PDBsum; 2B08; -. DR PDBsum; 2E86; -. DR PDBsum; 2FJS; -. DR PDBsum; 2P80; -. DR PDBsum; 2PP7; -. DR PDBsum; 2PP8; -. DR PDBsum; 2PP9; -. DR PDBsum; 2PPA; -. DR PDBsum; 2PPC; -. DR PDBsum; 2PPD; -. DR PDBsum; 2PPE; -. DR PDBsum; 2PPF; -. DR PDBsum; 3H4F; -. DR PDBsum; 3H4H; -. DR PDBsum; 3H56; -. DR PDBsum; 4YSC; -. DR PDBsum; 4YSE; -. DR PDBsum; 5D4H; -. DR PDBsum; 5D4I; -. DR PDBsum; 5D4J; -. DR PDBsum; 5F7A; -. DR PDBsum; 5F7B; -. DR AlphaFoldDB; P38501; -. DR BMRB; P38501; -. DR SMR; P38501; -. DR BRENDA; 1.7.2.1; 232. DR SABIO-RK; P38501; -. DR UniPathway; UPA00652; UER00707. DR EvolutionaryTrace; P38501; -. DR GO; GO:0042597; C:periplasmic space; IEA:UniProtKB-SubCell. DR GO; GO:0005507; F:copper ion binding; IEA:InterPro. DR GO; GO:0050421; F:nitrite reductase (NO-forming) activity; IEA:UniProtKB-EC. DR GO; GO:0019333; P:denitrification pathway; IEA:UniProtKB-UniPathway. DR GO; GO:0042128; P:nitrate assimilation; IEA:UniProtKB-KW. DR CDD; cd11020; CuRO_1_CuNIR; 1. DR Gene3D; 2.60.40.420; Cupredoxins - blue copper proteins; 2. DR InterPro; IPR011707; Cu-oxidase-like_N. DR InterPro; IPR001117; Cu-oxidase_2nd. DR InterPro; IPR008972; Cupredoxin. DR InterPro; IPR001287; NO2-reductase_Cu. DR InterPro; IPR006311; TAT_signal. DR NCBIfam; TIGR02376; Cu_nitrite_red; 1. DR Pfam; PF00394; Cu-oxidase; 1. DR Pfam; PF07732; Cu-oxidase_3; 1. DR PRINTS; PR00695; CUNO2RDTASE. DR SUPFAM; SSF49503; Cupredoxins; 2. DR PROSITE; PS51318; TAT; 1. PE 1: Evidence at protein level; KW 3D-structure; Copper; Direct protein sequencing; FAD; Flavoprotein; KW Metal-binding; Nitrate assimilation; Oxidoreductase; Periplasm; KW Pyrrolidone carboxylic acid; Repeat; Signal. FT SIGNAL 1..33 FT /note="Tat-type signal" FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00648, FT ECO:0000269|PubMed:8515232" FT CHAIN 34..376 FT /note="Copper-containing nitrite reductase" FT /id="PRO_0000002987" FT DOMAIN 34..211 FT /note="Plastocyanin-like 1" FT DOMAIN 212..376 FT /note="Plastocyanin-like 2" FT BINDING 131 FT /ligand="Cu cation" FT /ligand_id="ChEBI:CHEBI:23378" FT /ligand_label="1" FT /note="type 1 copper site" FT /evidence="ECO:0000269|PubMed:8172899" FT BINDING 136 FT /ligand="Cu cation" FT /ligand_id="ChEBI:CHEBI:23378" FT /ligand_label="2" FT /note="type 2 copper site" FT BINDING 171 FT /ligand="Cu cation" FT /ligand_id="ChEBI:CHEBI:23378" FT /ligand_label="2" FT /note="type 2 copper site" FT BINDING 172 FT /ligand="Cu cation" FT /ligand_id="ChEBI:CHEBI:23378" FT /ligand_label="1" FT /note="type 1 copper site" FT BINDING 181 FT /ligand="Cu cation" FT /ligand_id="ChEBI:CHEBI:23378" FT /ligand_label="1" FT /note="type 1 copper site" FT BINDING 186 FT /ligand="Cu cation" FT /ligand_id="ChEBI:CHEBI:23378" FT /ligand_label="1" FT /note="type 1 copper site" FT BINDING 342 FT /ligand="Cu cation" FT /ligand_id="ChEBI:CHEBI:23378" FT /ligand_label="2" FT /note="type 2 copper site" FT /evidence="ECO:0000269|PubMed:8172899" FT MOD_RES 34 FT /note="Pyrrolidone carboxylic acid" FT /evidence="ECO:0000269|PubMed:8515232" FT MUTAGEN 171 FT /note="H->K: Loses nitrite-reducing activity." FT /evidence="ECO:0000269|PubMed:8172899" FT MUTAGEN 186 FT /note="M->E: Contains only a type II copper atom and fails FT to catalyze the reduction of nitrite." FT /evidence="ECO:0000269|PubMed:8172899" FT HELIX 42..46 FT /evidence="ECO:0007829|PDB:4YSE" FT STRAND 50..52 FT /evidence="ECO:0007829|PDB:4YSE" FT STRAND 69..71 FT /evidence="ECO:0007829|PDB:5D4H" FT STRAND 74..87 FT /evidence="ECO:0007829|PDB:4YSE" FT STRAND 94..100 FT /evidence="ECO:0007829|PDB:4YSE" FT STRAND 103..105 FT /evidence="ECO:0007829|PDB:4YSE" FT STRAND 109..112 FT /evidence="ECO:0007829|PDB:4YSE" FT STRAND 116..123 FT /evidence="ECO:0007829|PDB:4YSE" FT HELIX 141..147 FT /evidence="ECO:0007829|PDB:4YSE" FT STRAND 154..161 FT /evidence="ECO:0007829|PDB:4YSE" FT STRAND 166..171 FT /evidence="ECO:0007829|PDB:4YSE" FT HELIX 178..183 FT /evidence="ECO:0007829|PDB:4YSE" FT STRAND 187..193 FT /evidence="ECO:0007829|PDB:4YSE" FT STRAND 209..219 FT /evidence="ECO:0007829|PDB:4YSE" FT HELIX 235..238 FT /evidence="ECO:0007829|PDB:4YSE" FT HELIX 239..246 FT /evidence="ECO:0007829|PDB:4YSE" FT TURN 247..249 FT /evidence="ECO:0007829|PDB:4YSE" FT STRAND 252..256 FT /evidence="ECO:0007829|PDB:4YSE" FT TURN 260..263 FT /evidence="ECO:0007829|PDB:4YSE" FT HELIX 265..267 FT /evidence="ECO:0007829|PDB:4YSE" FT STRAND 269..272 FT /evidence="ECO:0007829|PDB:4YSE" FT STRAND 276..286 FT /evidence="ECO:0007829|PDB:4YSE" FT STRAND 290..293 FT /evidence="ECO:0007829|PDB:4YSE" FT STRAND 297..301 FT /evidence="ECO:0007829|PDB:4YSE" FT STRAND 306..308 FT /evidence="ECO:0007829|PDB:2P80" FT STRAND 311..316 FT /evidence="ECO:0007829|PDB:4YSE" FT STRAND 323..330 FT /evidence="ECO:0007829|PDB:4YSE" FT STRAND 335..343 FT /evidence="ECO:0007829|PDB:4YSE" FT HELIX 344..348 FT /evidence="ECO:0007829|PDB:4YSE" FT STRAND 353..360 FT /evidence="ECO:0007829|PDB:4YSE" FT TURN 364..366 FT /evidence="ECO:0007829|PDB:4YSE" FT STRAND 367..375 FT /evidence="ECO:0007829|PDB:4YSE" SQ SEQUENCE 376 AA; 40332 MW; 0AD918988301BF29 CRC64; MAEQMQISRR TILAGAALAG ALAPVLATTS AWGQGAVRKA TAAEIAALPR QKVELVDPPF VHAHSQVAEG GPKVVEFTMV IEEKKIVIDD AGTEVHAMAF NGTVPGPLMV VHQDDYLELT LINPETNTLM HNIDFHAATG ALGGGGLTEI NPGEKTILRF KATKPGVFVY HCAPPGMVPW HVVSGMNGAI MVLPREGLHD GKGKALTYDK IYYVGEQDFY VPRDENGKYK KYEAPGDAYE DTVKVMRTLT PTHVVFNGAV GALTGDKAMT AAVGEKVLIV HSQANRDTRP HLIGGHGDYV WATGKFNTPP DVDQETWFIP GGAAGAAFYT FQQPGIYAYV NHNLIEAFEL GAAAHFKVTG EWNDDLMTSV LAPSGT //