NIRK_RHIME
ID NIRK_RHIME Reviewed; 376 AA.
AC Q92Z29;
DT 25-MAR-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2001, sequence version 1.
DT 03-AUG-2022, entry version 117.
DE RecName: Full=Copper-containing nitrite reductase;
DE EC=1.7.2.1;
DE AltName: Full=Cu-NIR;
DE Flags: Precursor;
GN Name=nirK; OrderedLocusNames=RA0681; ORFNames=SMa1250;
OS Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium
OS meliloti).
OG Plasmid pSymA (megaplasmid 1).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Sinorhizobium/Ensifer group; Sinorhizobium.
OX NCBI_TaxID=266834;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=1021;
RX PubMed=11481432; DOI=10.1073/pnas.161294798;
RA Barnett M.J., Fisher R.F., Jones T., Komp C., Abola A.P., Barloy-Hubler F.,
RA Bowser L., Capela D., Galibert F., Gouzy J., Gurjal M., Hong A., Huizar L.,
RA Hyman R.W., Kahn D., Kahn M.L., Kalman S., Keating D.H., Palm C.,
RA Peck M.C., Surzycki R., Wells D.H., Yeh K.-C., Davis R.W., Federspiel N.A.,
RA Long S.R.;
RT "Nucleotide sequence and predicted functions of the entire Sinorhizobium
RT meliloti pSymA megaplasmid.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:9883-9888(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=1021;
RX PubMed=11474104; DOI=10.1126/science.1060966;
RA Galibert F., Finan T.M., Long S.R., Puehler A., Abola P., Ampe F.,
RA Barloy-Hubler F., Barnett M.J., Becker A., Boistard P., Bothe G.,
RA Boutry M., Bowser L., Buhrmester J., Cadieu E., Capela D., Chain P.,
RA Cowie A., Davis R.W., Dreano S., Federspiel N.A., Fisher R.F., Gloux S.,
RA Godrie T., Goffeau A., Golding B., Gouzy J., Gurjal M., Hernandez-Lucas I.,
RA Hong A., Huizar L., Hyman R.W., Jones T., Kahn D., Kahn M.L., Kalman S.,
RA Keating D.H., Kiss E., Komp C., Lelaure V., Masuy D., Palm C., Peck M.C.,
RA Pohl T.M., Portetelle D., Purnelle B., Ramsperger U., Surzycki R.,
RA Thebault P., Vandenbol M., Vorhoelter F.J., Weidner S., Wells D.H.,
RA Wong K., Yeh K.-C., Batut J.;
RT "The composite genome of the legume symbiont Sinorhizobium meliloti.";
RL Science 293:668-672(2001).
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. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Periplasm {ECO:0000250}.
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 not been experimentally proven.
CC -!- SIMILARITY: Belongs to the multicopper oxidase family. {ECO:0000305}.
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DR EMBL; AE006469; AAK65339.1; -; Genomic_DNA.
DR PIR; A95347; A95347.
DR RefSeq; NP_435927.1; NC_003037.1.
DR RefSeq; WP_010967660.1; NC_003037.1.
DR AlphaFoldDB; Q92Z29; -.
DR SMR; Q92Z29; -.
DR EnsemblBacteria; AAK65339; AAK65339; SMa1250.
DR GeneID; 25011644; -.
DR GeneID; 61599449; -.
DR KEGG; sme:SMa1250; -.
DR PATRIC; fig|266834.11.peg.701; -.
DR HOGENOM; CLU_031740_1_0_5; -.
DR OMA; APCVGCK; -.
DR UniPathway; UPA00652; UER00707.
DR PRO; PR:Q92Z29; -.
DR Proteomes; UP000001976; Plasmid pSymA.
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 3: Inferred from homology;
KW Copper; FAD; Flavoprotein; Metal-binding; Nitrate assimilation;
KW Oxidoreductase; Periplasm; Plasmid; Reference proteome; Repeat; Signal.
FT SIGNAL 1..33
FT /note="Tat-type signal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00648"
FT CHAIN 34..376
FT /note="Copper-containing nitrite reductase"
FT /id="PRO_0000002991"
FT DOMAIN 98..193
FT /note="Plastocyanin-like 1"
FT DOMAIN 258..359
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:0000250"
FT BINDING 136
FT /ligand="Cu cation"
FT /ligand_id="ChEBI:CHEBI:23378"
FT /ligand_label="2"
FT /note="type 2 copper site"
FT /evidence="ECO:0000250"
FT BINDING 171
FT /ligand="Cu cation"
FT /ligand_id="ChEBI:CHEBI:23378"
FT /ligand_label="2"
FT /note="type 2 copper site"
FT /evidence="ECO:0000250"
FT BINDING 172
FT /ligand="Cu cation"
FT /ligand_id="ChEBI:CHEBI:23378"
FT /ligand_label="1"
FT /note="type 1 copper site"
FT /evidence="ECO:0000250"
FT BINDING 181
FT /ligand="Cu cation"
FT /ligand_id="ChEBI:CHEBI:23378"
FT /ligand_label="1"
FT /note="type 1 copper site"
FT /evidence="ECO:0000250"
FT BINDING 186
FT /ligand="Cu cation"
FT /ligand_id="ChEBI:CHEBI:23378"
FT /ligand_label="1"
FT /note="type 1 copper site"
FT /evidence="ECO:0000250"
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:0000250"
SQ SEQUENCE 376 AA; 40259 MW; 9B7999273001DC63 CRC64;
MSEQFQMTRR SMLAGAAIAG AVTPLIGAVS AHAEEAVAKT AHINVASLPR VKVDLVKPPF
VHAHTQKAEG GPKVVEFTLT IEEKKIVIDE QGTELHAMTF NGSVPGPLMV VHQDDYVELT
LINPDTNTLQ HNIDFHSATG ALGGGALTVV NPGDTTVLRF KASKAGVFVY HCAPPGMVPW
HVTSGMNGAI MVLPREGLTD GKGNSITYDK VYYVGEQDFY VPRDANGKFK KYESVGEAYA
DTLEVMRTLT PSHIVFNGAV GALTGDSALK AAVGEKVLIV HSQANRDTRP HLIGGHGDYV
WATGKFRNAP DVDQETWFIP GGTAGAAFYT FEQPGIYAYV NHNLIEAFEL GAAAHFAVTG
DWNDDLMTSV RAPSGT
