NIR_ALCFA
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 03-AUG-2022, entry version 121.
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; Proteobacteria; 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}.
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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 Gene3D; 2.60.40.420; -; 2.
DR InterPro; IPR001117; Cu-oxidase.
DR InterPro; IPR011707; Cu-oxidase_N.
DR InterPro; IPR008972; Cupredoxin.
DR InterPro; IPR001287; NO2-reductase_Cu.
DR InterPro; IPR006311; TAT_signal.
DR Pfam; PF00394; Cu-oxidase; 1.
DR Pfam; PF07732; Cu-oxidase_3; 1.
DR PRINTS; PR00695; CUNO2RDTASE.
DR SUPFAM; SSF49503; SSF49503; 2.
DR TIGRFAMs; TIGR02376; Cu_nitrite_red; 1.
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
