NIR_CERS5
ID NIR_CERS5 Reviewed; 374 AA.
AC Q53239; A4WSX4;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 23-OCT-2007, sequence version 2.
DT 03-AUG-2022, entry version 133.
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=Rsph17025_1595;
OS Cereibacter sphaeroides (strain ATCC 17025 / ATH 2.4.3) (Rhodobacter
OS sphaeroides).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC Rhodobacteraceae; Cereibacter.
OX NCBI_TaxID=349102;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=9023188; DOI=10.1128/jb.179.4.1090-1095.1997;
RA Tosques I.E., Kwiatkowski A.V., Shi J., Shapleigh J.P.;
RT "Characterization and regulation of the gene encoding nitrite reductase in
RT Rhodobacter sphaeroides 2.4.3.";
RL J. Bacteriol. 179:1090-1095(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 17025 / ATH 2.4.3;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA Chertkov O., Brettin T., Bruce D., Han C., Schmutz J., Larimer F., Land M.,
RA Hauser L., Kyrpides N., Kim E., Richardson P., Mackenzie C., Choudhary M.,
RA Donohue T.J., Kaplan S.;
RT "Complete sequence of chromosome of Rhodobacter sphaeroides ATCC 17025.";
RL Submitted (APR-2007) to the EMBL/GenBank/DDBJ databases.
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; U62291; AAB05767.1; -; Genomic_DNA.
DR EMBL; CP000661; ABP70488.1; -; Genomic_DNA.
DR PDB; 1MZY; X-ray; 1.46 A; A=39-371.
DR PDB; 1MZZ; X-ray; 2.00 A; A/B/C=39-371.
DR PDB; 1N70; X-ray; 1.60 A; A=41-374.
DR PDB; 1ZV2; X-ray; 1.74 A; A=44-371.
DR PDB; 2A3T; X-ray; 1.85 A; A=44-371.
DR PDB; 2DWS; X-ray; 1.85 A; A=44-371.
DR PDB; 2DWT; X-ray; 1.90 A; A=44-372.
DR PDB; 2DY2; X-ray; 2.26 A; A=44-372.
DR PDBsum; 1MZY; -.
DR PDBsum; 1MZZ; -.
DR PDBsum; 1N70; -.
DR PDBsum; 1ZV2; -.
DR PDBsum; 2A3T; -.
DR PDBsum; 2DWS; -.
DR PDBsum; 2DWT; -.
DR PDBsum; 2DY2; -.
DR AlphaFoldDB; Q53239; -.
DR SMR; Q53239; -.
DR STRING; 349102.Rsph17025_1595; -.
DR EnsemblBacteria; ABP70488; ABP70488; Rsph17025_1595.
DR KEGG; rsq:Rsph17025_1595; -.
DR eggNOG; COG2132; Bacteria.
DR HOGENOM; CLU_031740_1_0_5; -.
DR OMA; APCVGCK; -.
DR OrthoDB; 971126at2; -.
DR BioCyc; RSPH349102:G1G8M-1642-MON; -.
DR UniPathway; UPA00652; UER00707.
DR EvolutionaryTrace; Q53239; -.
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; FAD; Flavoprotein; Metal-binding;
KW Nitrate assimilation; Oxidoreductase; Periplasm; Repeat; Signal.
FT SIGNAL 1..31
FT /note="Tat-type signal"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00648"
FT CHAIN 32..374
FT /note="Copper-containing nitrite reductase"
FT /id="PRO_0000002992"
FT DOMAIN 93..189
FT /note="Plastocyanin-like 1"
FT DOMAIN 254..355
FT /note="Plastocyanin-like 2"
FT BINDING 126
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 131
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 166
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 167
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 177
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 182
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 338
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 CONFLICT 27
FT /note="E -> Q (in Ref. 1; AAB05767)"
FT /evidence="ECO:0000305"
FT CONFLICT 230
FT /note="D -> T (in Ref. 1; AAB05767)"
FT /evidence="ECO:0000305"
FT CONFLICT 281
FT /note="N -> K (in Ref. 1; AAB05767)"
FT /evidence="ECO:0000305"
FT CONFLICT 319
FT /note="S -> T (in Ref. 1; AAB05767)"
FT /evidence="ECO:0000305"
FT CONFLICT 351
FT /note="H -> S (in Ref. 1; AAB05767)"
FT /evidence="ECO:0000305"
FT CONFLICT 367..368
FT /note="VA -> WP (in Ref. 1; AAB05767)"
FT /evidence="ECO:0000305"
FT STRAND 46..48
FT /evidence="ECO:0007829|PDB:1MZY"
FT STRAND 65..67
FT /evidence="ECO:0007829|PDB:1MZY"
FT STRAND 70..85
FT /evidence="ECO:0007829|PDB:1MZY"
FT STRAND 88..95
FT /evidence="ECO:0007829|PDB:1MZY"
FT STRAND 98..100
FT /evidence="ECO:0007829|PDB:1MZY"
FT STRAND 103..107
FT /evidence="ECO:0007829|PDB:1MZY"
FT STRAND 111..118
FT /evidence="ECO:0007829|PDB:1MZY"
FT HELIX 136..142
FT /evidence="ECO:0007829|PDB:1MZY"
FT STRAND 149..156
FT /evidence="ECO:0007829|PDB:1MZY"
FT STRAND 161..166
FT /evidence="ECO:0007829|PDB:1MZY"
FT HELIX 173..179
FT /evidence="ECO:0007829|PDB:1MZY"
FT STRAND 183..189
FT /evidence="ECO:0007829|PDB:1MZY"
FT STRAND 205..215
FT /evidence="ECO:0007829|PDB:1MZY"
FT STRAND 223..225
FT /evidence="ECO:0007829|PDB:2DY2"
FT HELIX 231..242
FT /evidence="ECO:0007829|PDB:1MZY"
FT TURN 243..245
FT /evidence="ECO:0007829|PDB:1MZY"
FT STRAND 248..252
FT /evidence="ECO:0007829|PDB:1MZY"
FT TURN 256..259
FT /evidence="ECO:0007829|PDB:1MZY"
FT HELIX 261..263
FT /evidence="ECO:0007829|PDB:1MZY"
FT STRAND 265..268
FT /evidence="ECO:0007829|PDB:1MZY"
FT STRAND 272..282
FT /evidence="ECO:0007829|PDB:1MZY"
FT STRAND 286..289
FT /evidence="ECO:0007829|PDB:1MZY"
FT STRAND 293..297
FT /evidence="ECO:0007829|PDB:1MZY"
FT STRAND 307..312
FT /evidence="ECO:0007829|PDB:1MZY"
FT STRAND 319..326
FT /evidence="ECO:0007829|PDB:1MZY"
FT STRAND 331..339
FT /evidence="ECO:0007829|PDB:1MZY"
FT HELIX 340..344
FT /evidence="ECO:0007829|PDB:1MZY"
FT STRAND 349..356
FT /evidence="ECO:0007829|PDB:1MZY"
FT TURN 360..362
FT /evidence="ECO:0007829|PDB:1MZY"
FT STRAND 363..371
FT /evidence="ECO:0007829|PDB:1MZZ"
SQ SEQUENCE 374 AA; 40232 MW; BD0FACA94A991F3B CRC64;
MFTRRAALVG AAALASAPLV IRTAGAEEAP AQLASAAPVD LSNLPRVKHT LVPPPFAHAH
EQVAASGPVI NEFEMRIIEK EVQLDEDAYL QAMTFDGSIP GPLMIVHEGD YVELTLINPP
ENTMPHNIDF HAATGALGGG GLTLINPGEK VVLRFKATRA GAFVYHCAPG GPMIPWHVVS
GMAGCIMVLP RDGLKDHEGK PVRYDTVYYI GESDHYIPKD EDGTYMRFSD PSEGYEDMVA
VMDTLIPSHI VFNGAVGALT GEGALKAKVG DNVLFVHSQP NRDSRPHLIG GHGDLVWETG
KFHNAPERDL ETWFIRGGSA GAALYKFLQP GVYAYVNHNL IEAVHKGATA HVLVEGEWDN
DLMEQVVAPV GLTG
