NIR_ACHCY
ID NIR_ACHCY Reviewed; 378 AA.
AC P25006;
DT 01-MAR-1992, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 03-AUG-2022, entry version 129.
DE RecName: Full=Copper-containing nitrite reductase;
DE EC=1.7.2.1;
DE AltName: Full=Cu-NIR;
DE Flags: Precursor;
GN Name=nirK;
OS Achromobacter cycloclastes.
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Alcaligenaceae; Achromobacter.
OX NCBI_TaxID=223;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=ATCC 21921 / JCM 20009 / IAM 1013 / KCTC 2947 / LMG 1127 / NBRC
RC 102459 / An-17;
RX PubMed=8605003; DOI=10.1006/bbrc.1996.0249;
RA Chen J.-Y., Chang W.-C., Chang T., Chang W.-C., Liu M.-Y., Payne W.J.,
RA le Gall J.;
RT "Cloning, characterization, and expression of the nitric oxide-generating
RT nitrite reductase and of the blue copper protein genes of Achromobacter
RT cycloclastes.";
RL Biochem. Biophys. Res. Commun. 219:423-428(1996).
RN [2]
RP PROTEIN SEQUENCE OF 39-378.
RC STRAIN=ATCC 21921 / JCM 20009 / IAM 1013 / KCTC 2947 / LMG 1127 / NBRC
RC 102459 / An-17;
RX PubMed=1830217; DOI=10.1021/bi00243a020;
RA Fenderson F.F., Kumar S., Adman E.T., Liu M.-Y., Payne W.J., le Gall J.;
RT "Amino acid sequence of nitrite reductase: a copper protein from
RT Achromobacter cycloclastes.";
RL Biochemistry 30:7180-7185(1991).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
RX PubMed=1862344; DOI=10.1126/science.1862344;
RA Godden J.W., Turley S., Teller D.C., Adman E.T., Liu M.-Y., Payne W.J.,
RA le Gall J.;
RT "The 2.3-A X-ray structure of nitrite reductase from Achromobacter
RT cycloclastes.";
RL Science 253:438-442(1991).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
RX PubMed=7499203; DOI=10.1074/jbc.270.46.27458;
RA Adman E.T., Godden J.W., Turley S.;
RT "The structure of copper-nitrite reductase from Achromobacter cycloclastes
RT at five pH values, with NO2-bound and with type II copper depleted.";
RL J. Biol. Chem. 270:27458-27474(1995).
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(+); Xref=ChEBI:CHEBI:49552;
CC Note=Binds 1 Cu(+) ion.;
CC -!- COFACTOR:
CC Name=Cu(2+); Xref=ChEBI:CHEBI:29036;
CC Note=Binds 1 Cu(2+) ion.;
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC -!- PATHWAY: Nitrogen metabolism; nitrate reduction (denitrification);
CC dinitrogen from nitrate: step 2/4.
CC -!- SUBUNIT: Homotrimer.
CC -!- SUBCELLULAR LOCATION: Periplasm.
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; Z48635; CAA88564.1; -; Genomic_DNA.
DR PIR; JC4648; JC4648.
DR PDB; 1KCB; X-ray; 1.65 A; A=39-378.
DR PDB; 1NIA; X-ray; 2.50 A; A/B/C=39-378.
DR PDB; 1NIB; X-ray; 2.70 A; A/B/C=39-378.
DR PDB; 1NIC; X-ray; 1.90 A; A=39-378.
DR PDB; 1NID; X-ray; 2.20 A; A=39-378.
DR PDB; 1NIE; X-ray; 1.90 A; A=39-378.
DR PDB; 1NIF; X-ray; 1.70 A; A=39-378.
DR PDB; 1RZP; X-ray; 1.90 A; A/B/C=39-373.
DR PDB; 1RZQ; X-ray; 2.20 A; A/B/C=39-373.
DR PDB; 2AVF; X-ray; 2.60 A; A/B/C/D/E/F=39-367.
DR PDB; 2BW4; X-ray; 0.90 A; A=39-378.
DR PDB; 2BW5; X-ray; 1.12 A; A=39-378.
DR PDB; 2BWD; X-ray; 1.15 A; A=39-378.
DR PDB; 2BWI; X-ray; 1.10 A; A=39-378.
DR PDB; 2NRD; X-ray; 2.10 A; A=39-378.
DR PDB; 2Y1A; X-ray; 1.95 A; A=39-378.
DR PDB; 5AKR; X-ray; 0.87 A; A=1-378.
DR PDB; 5I6K; X-ray; 1.07 A; A=45-378.
DR PDB; 5I6L; X-ray; 1.08 A; A=46-377.
DR PDB; 5I6M; X-ray; 1.09 A; A=46-377.
DR PDB; 5I6N; X-ray; 1.22 A; A=46-377.
DR PDB; 5I6O; X-ray; 1.45 A; A=46-377.
DR PDB; 5I6P; X-ray; 1.56 A; A=46-377.
DR PDB; 5N8F; X-ray; 1.38 A; A=45-378.
DR PDB; 5N8G; X-ray; 1.47 A; A=45-378.
DR PDB; 5N8H; X-ray; 1.65 A; A=45-378.
DR PDB; 5N8I; X-ray; 1.40 A; A=45-378.
DR PDB; 5OF5; X-ray; 1.08 A; A=45-378.
DR PDB; 5OF6; X-ray; 1.08 A; A=45-378.
DR PDB; 5OF7; X-ray; 1.27 A; A=45-378.
DR PDB; 5OF8; X-ray; 1.34 A; A=45-378.
DR PDB; 5OFC; X-ray; 1.68 A; A=45-378.
DR PDB; 5OFD; X-ray; 1.77 A; A=45-378.
DR PDB; 5OFE; X-ray; 1.84 A; A=45-378.
DR PDB; 5OFF; X-ray; 1.41 A; A=45-378.
DR PDB; 5OFG; X-ray; 1.49 A; A=45-378.
DR PDB; 5OFH; X-ray; 1.58 A; A=45-378.
DR PDB; 5OG2; X-ray; 1.64 A; A=45-378.
DR PDB; 5OG3; X-ray; 1.70 A; A=45-378.
DR PDB; 5OG4; X-ray; 1.76 A; A=45-378.
DR PDB; 5OG5; X-ray; 1.82 A; A=45-378.
DR PDB; 5OG6; X-ray; 1.85 A; A=45-378.
DR PDB; 5OGF; X-ray; 1.88 A; A=46-378.
DR PDB; 5OGG; X-ray; 1.91 A; A=45-378.
DR PDB; 6GB8; X-ray; 1.48 A; A=39-378.
DR PDB; 6GBB; X-ray; 1.48 A; A=39-378.
DR PDB; 6GBY; X-ray; 1.48 A; A=1-378.
DR PDB; 6GCG; X-ray; 1.80 A; A=1-378.
DR PDB; 6GSQ; X-ray; 1.50 A; A=1-378.
DR PDB; 6GT0; X-ray; 1.50 A; A=1-378.
DR PDB; 6GT2; X-ray; 1.60 A; A=1-378.
DR PDB; 6GTI; X-ray; 1.50 A; A=1-378.
DR PDB; 6GTJ; Neutron; 1.80 A; A=39-378.
DR PDB; 6GTK; X-ray; 1.50 A; A=1-378.
DR PDB; 6GTL; X-ray; 1.50 A; A=1-378.
DR PDB; 6GTN; X-ray; 1.50 A; A=1-378.
DR PDB; 6KNF; EM; 2.99 A; A/B/C=45-378.
DR PDB; 6KNG; EM; 2.85 A; A/B/C=45-378.
DR PDB; 6QWG; X-ray; 1.90 A; A=46-378.
DR PDB; 6ZU6; X-ray; 1.15 A; A=45-378.
DR PDB; 6ZUA; X-ray; 1.14 A; A=45-378.
DR PDB; 6ZUB; X-ray; 1.08 A; A=45-378.
DR PDB; 6ZUD; X-ray; 1.10 A; A=45-378.
DR PDB; 6ZUT; X-ray; 1.15 A; A=45-378.
DR PDBsum; 1KCB; -.
DR PDBsum; 1NIA; -.
DR PDBsum; 1NIB; -.
DR PDBsum; 1NIC; -.
DR PDBsum; 1NID; -.
DR PDBsum; 1NIE; -.
DR PDBsum; 1NIF; -.
DR PDBsum; 1RZP; -.
DR PDBsum; 1RZQ; -.
DR PDBsum; 2AVF; -.
DR PDBsum; 2BW4; -.
DR PDBsum; 2BW5; -.
DR PDBsum; 2BWD; -.
DR PDBsum; 2BWI; -.
DR PDBsum; 2NRD; -.
DR PDBsum; 2Y1A; -.
DR PDBsum; 5AKR; -.
DR PDBsum; 5I6K; -.
DR PDBsum; 5I6L; -.
DR PDBsum; 5I6M; -.
DR PDBsum; 5I6N; -.
DR PDBsum; 5I6O; -.
DR PDBsum; 5I6P; -.
DR PDBsum; 5N8F; -.
DR PDBsum; 5N8G; -.
DR PDBsum; 5N8H; -.
DR PDBsum; 5N8I; -.
DR PDBsum; 5OF5; -.
DR PDBsum; 5OF6; -.
DR PDBsum; 5OF7; -.
DR PDBsum; 5OF8; -.
DR PDBsum; 5OFC; -.
DR PDBsum; 5OFD; -.
DR PDBsum; 5OFE; -.
DR PDBsum; 5OFF; -.
DR PDBsum; 5OFG; -.
DR PDBsum; 5OFH; -.
DR PDBsum; 5OG2; -.
DR PDBsum; 5OG3; -.
DR PDBsum; 5OG4; -.
DR PDBsum; 5OG5; -.
DR PDBsum; 5OG6; -.
DR PDBsum; 5OGF; -.
DR PDBsum; 5OGG; -.
DR PDBsum; 6GB8; -.
DR PDBsum; 6GBB; -.
DR PDBsum; 6GBY; -.
DR PDBsum; 6GCG; -.
DR PDBsum; 6GSQ; -.
DR PDBsum; 6GT0; -.
DR PDBsum; 6GT2; -.
DR PDBsum; 6GTI; -.
DR PDBsum; 6GTJ; -.
DR PDBsum; 6GTK; -.
DR PDBsum; 6GTL; -.
DR PDBsum; 6GTN; -.
DR PDBsum; 6KNF; -.
DR PDBsum; 6KNG; -.
DR PDBsum; 6QWG; -.
DR PDBsum; 6ZU6; -.
DR PDBsum; 6ZUA; -.
DR PDBsum; 6ZUB; -.
DR PDBsum; 6ZUD; -.
DR PDBsum; 6ZUT; -.
DR AlphaFoldDB; P25006; -.
DR SMR; P25006; -.
DR DrugBank; DB03814; 2-(N-morpholino)ethanesulfonic acid.
DR KEGG; ag:CAA88564; -.
DR BRENDA; 1.7.2.1; 69.
DR SABIO-RK; P25006; -.
DR UniPathway; UPA00652; UER00707.
DR EvolutionaryTrace; P25006; -.
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; IPR045087; Cu-oxidase_fam.
DR InterPro; IPR011707; Cu-oxidase_N.
DR InterPro; IPR008972; Cupredoxin.
DR InterPro; IPR001287; NO2-reductase_Cu.
DR InterPro; IPR006311; TAT_signal.
DR PANTHER; PTHR11709; PTHR11709; 1.
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; Repeat;
KW Signal.
FT SIGNAL 1..38
FT /note="Tat-type signal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00648,
FT ECO:0000269|PubMed:1830217"
FT CHAIN 39..378
FT /note="Copper-containing nitrite reductase"
FT /id="PRO_0000002986"
FT DOMAIN 39..213
FT /note="Plastocyanin-like 1"
FT DOMAIN 214..378
FT /note="Plastocyanin-like 2"
FT BINDING 133
FT /ligand="Cu cation"
FT /ligand_id="ChEBI:CHEBI:23378"
FT /ligand_label="1"
FT /note="type 1 copper site"
FT BINDING 138
FT /ligand="Cu cation"
FT /ligand_id="ChEBI:CHEBI:23378"
FT /ligand_label="2"
FT /note="type 2 copper site"
FT BINDING 173
FT /ligand="Cu cation"
FT /ligand_id="ChEBI:CHEBI:23378"
FT /ligand_label="2"
FT /note="type 2 copper site"
FT BINDING 174
FT /ligand="Cu cation"
FT /ligand_id="ChEBI:CHEBI:23378"
FT /ligand_label="1"
FT /note="type 1 copper site"
FT BINDING 183
FT /ligand="Cu cation"
FT /ligand_id="ChEBI:CHEBI:23378"
FT /ligand_label="1"
FT /note="type 1 copper site"
FT BINDING 188
FT /ligand="Cu cation"
FT /ligand_id="ChEBI:CHEBI:23378"
FT /ligand_label="1"
FT /note="type 1 copper site"
FT BINDING 344
FT /ligand="Cu cation"
FT /ligand_id="ChEBI:CHEBI:23378"
FT /ligand_label="2"
FT /note="type 2 copper site"
FT HELIX 47..49
FT /evidence="ECO:0007829|PDB:5AKR"
FT STRAND 52..54
FT /evidence="ECO:0007829|PDB:5AKR"
FT STRAND 71..73
FT /evidence="ECO:0007829|PDB:5AKR"
FT STRAND 76..89
FT /evidence="ECO:0007829|PDB:5AKR"
FT STRAND 91..93
FT /evidence="ECO:0007829|PDB:6KNG"
FT STRAND 96..102
FT /evidence="ECO:0007829|PDB:5AKR"
FT STRAND 105..107
FT /evidence="ECO:0007829|PDB:5AKR"
FT STRAND 111..114
FT /evidence="ECO:0007829|PDB:5AKR"
FT STRAND 118..125
FT /evidence="ECO:0007829|PDB:5AKR"
FT STRAND 135..140
FT /evidence="ECO:0007829|PDB:2AVF"
FT HELIX 143..149
FT /evidence="ECO:0007829|PDB:5AKR"
FT STRAND 156..163
FT /evidence="ECO:0007829|PDB:5AKR"
FT STRAND 168..173
FT /evidence="ECO:0007829|PDB:5AKR"
FT TURN 177..179
FT /evidence="ECO:0007829|PDB:2AVF"
FT HELIX 180..185
FT /evidence="ECO:0007829|PDB:5AKR"
FT STRAND 189..195
FT /evidence="ECO:0007829|PDB:5AKR"
FT STRAND 203..205
FT /evidence="ECO:0007829|PDB:6KNG"
FT STRAND 211..221
FT /evidence="ECO:0007829|PDB:5AKR"
FT STRAND 227..229
FT /evidence="ECO:0007829|PDB:5N8I"
FT HELIX 237..249
FT /evidence="ECO:0007829|PDB:5AKR"
FT STRAND 254..258
FT /evidence="ECO:0007829|PDB:5AKR"
FT TURN 262..265
FT /evidence="ECO:0007829|PDB:5AKR"
FT HELIX 267..269
FT /evidence="ECO:0007829|PDB:5AKR"
FT STRAND 271..274
FT /evidence="ECO:0007829|PDB:5AKR"
FT STRAND 278..288
FT /evidence="ECO:0007829|PDB:5AKR"
FT STRAND 292..295
FT /evidence="ECO:0007829|PDB:5AKR"
FT STRAND 299..303
FT /evidence="ECO:0007829|PDB:5AKR"
FT STRAND 313..317
FT /evidence="ECO:0007829|PDB:5AKR"
FT STRAND 325..332
FT /evidence="ECO:0007829|PDB:5AKR"
FT STRAND 337..345
FT /evidence="ECO:0007829|PDB:5AKR"
FT HELIX 346..350
FT /evidence="ECO:0007829|PDB:5AKR"
FT STRAND 355..362
FT /evidence="ECO:0007829|PDB:5AKR"
FT TURN 366..368
FT /evidence="ECO:0007829|PDB:5AKR"
FT STRAND 369..371
FT /evidence="ECO:0007829|PDB:1RZP"
SQ SEQUENCE 378 AA; 40771 MW; A70B52B814090EA5 CRC64;
MTEQLQMTRR TMLAGAALAG AVAPLLHTAQ AHAAGAAAAA GAAPVDISTL PRVKVDLVKP
PFVHAHDQVA KTGPRVVEFT MTIEEKKLVI DREGTEIHAM TFNGSVPGPL MVVHENDYVE
LRLINPDTNT LLHNIDFHAA TGALGGGALT QVNPGEETTL RFKATKPGVF VYHCAPEGMV
PWHVTSGMNG AIMVLPRDGL KDEKGQPLTY DKIYYVGEQD FYVPKDEAGN YKKYETPGEA
YEDAVKAMRT LTPTHIVFNG AVGALTGDHA LTAAVGERVL VVHSQANRDT RPHLIGGHGD
YVWATGKFRN PPDLDQETWL IPGGTAGAAF YTFRQPGVYA YVNHNLIEAF ELGAAGHFKV
TGEWNDDLMT SVVKPASM
