NIRS_PARDP
ID NIRS_PARDP Reviewed; 596 AA.
AC Q51700; A1B4Y0;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 135.
DE RecName: Full=Nitrite reductase;
DE EC=1.7.2.1;
DE AltName: Full=Cytochrome cd1;
DE AltName: Full=Cytochrome oxidase;
DE AltName: Full=Hydroxylamine reductase;
DE EC=1.7.99.1;
DE Flags: Precursor;
GN Name=nirS; OrderedLocusNames=Pden_2487;
OS Paracoccus denitrificans (strain Pd 1222).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC Rhodobacteraceae; Paracoccus.
OX NCBI_TaxID=318586;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=7747927; DOI=10.1007/bf00871635;
RA de Boer A.P.N., Reijnders W.N.M., Kuenen J.G., Stouthamer A.H.,
RA van Spanning R.J.M.;
RT "Isolation, sequencing and mutational analysis of a gene cluster involved
RT in nitrite reduction in Paracoccus denitrificans.";
RL Antonie Van Leeuwenhoek 66:111-127(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Pd 1222;
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 Munk A.C., Brettin T., Bruce D., Han C., Tapia R., Gilna P., Schmutz J.,
RA Larimer F., Land M., Hauser L., Kyrpides N., Lykidis A., Spiro S.,
RA Richardson D.J., Moir J.W.B., Ferguson S.J., van Spanning R.J.M.,
RA Richardson P.;
RT "Complete sequence of chromosome 1 of Paracoccus denitrificans PD1222.";
RL Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Inactivation of this cytochrome oxidase results in the loss
CC of nitrite and nitric oxide reductase activities, but not of nitrous
CC oxide reductase activity.
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 -!- CATALYTIC ACTIVITY:
CC Reaction=A + H2O + NH4(+) = AH2 + H(+) + hydroxylamine;
CC Xref=Rhea:RHEA:22052, ChEBI:CHEBI:13193, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:15429, ChEBI:CHEBI:17499,
CC ChEBI:CHEBI:28938; EC=1.7.99.1;
CC -!- COFACTOR:
CC Name=heme c; Xref=ChEBI:CHEBI:61717;
CC Evidence={ECO:0000250|UniProtKB:P72181};
CC Note=Binds 1 heme c group covalently per subunit.
CC {ECO:0000250|UniProtKB:P72181};
CC -!- COFACTOR:
CC Name=heme; Xref=ChEBI:CHEBI:30413;
CC Evidence={ECO:0000250|UniProtKB:P72181};
CC Note=Binds 1 heme d1 group per subunit. {ECO:0000250|UniProtKB:P72181};
CC -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Periplasm {ECO:0000250}.
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DR EMBL; U05002; AAA93118.1; -; Genomic_DNA.
DR EMBL; CP000489; ABL70574.1; -; Genomic_DNA.
DR RefSeq; WP_011748767.1; NC_008686.1.
DR AlphaFoldDB; Q51700; -.
DR SMR; Q51700; -.
DR STRING; 318586.Pden_2487; -.
DR PRIDE; Q51700; -.
DR EnsemblBacteria; ABL70574; ABL70574; Pden_2487.
DR KEGG; pde:Pden_2487; -.
DR eggNOG; COG2010; Bacteria.
DR HOGENOM; CLU_025262_0_0_5; -.
DR OMA; MPNWGTS; -.
DR Proteomes; UP000000361; Chromosome 1.
DR GO; GO:0042597; C:periplasmic space; IEA:UniProtKB-SubCell.
DR GO; GO:0009055; F:electron transfer activity; IEA:InterPro.
DR GO; GO:0020037; F:heme binding; IEA:InterPro.
DR GO; GO:0050418; F:hydroxylamine reductase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0050421; F:nitrite reductase (NO-forming) activity; IEA:UniProtKB-EC.
DR Gene3D; 1.10.760.10; -; 1.
DR Gene3D; 2.140.10.20; -; 1.
DR InterPro; IPR009056; Cyt_c-like_dom.
DR InterPro; IPR036909; Cyt_c-like_dom_sf.
DR InterPro; IPR003143; Cyt_cd1_C_sf.
DR InterPro; IPR011048; Haem_d1_sf.
DR Pfam; PF13442; Cytochrome_CBB3; 1.
DR SUPFAM; SSF46626; SSF46626; 1.
DR SUPFAM; SSF51004; SSF51004; 1.
DR PROSITE; PS51007; CYTC; 1.
PE 3: Inferred from homology;
KW Electron transport; Heme; Iron; Metal-binding; Oxidoreductase; Periplasm;
KW Reference proteome; Signal; Transport.
FT SIGNAL 1..29
FT /evidence="ECO:0000250"
FT CHAIN 30..596
FT /note="Nitrite reductase"
FT /id="PRO_0000006574"
FT DOMAIN 77..162
FT /note="Cytochrome c"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00433"
FT REGION 30..76
FT /note="N-terminal tail"
FT REGION 163..596
FT /note="D1-heme domain"
FT BINDING 46
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000250|UniProtKB:P72181"
FT BINDING 54
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000250|UniProtKB:P72181"
FT BINDING 57
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000250|UniProtKB:P72181"
FT BINDING 94
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /note="covalent"
FT /evidence="ECO:0000250|UniProtKB:P72181"
FT BINDING 97
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /note="covalent"
FT /evidence="ECO:0000250|UniProtKB:P72181"
FT BINDING 98
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000250|UniProtKB:P72181"
FT BINDING 108
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /evidence="ECO:0000250|UniProtKB:P72181"
FT BINDING 122
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /evidence="ECO:0000250|UniProtKB:P72181"
FT BINDING 138
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000250|UniProtKB:P72181"
FT BINDING 203
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000250|UniProtKB:P72181"
FT BINDING 229
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000250|UniProtKB:P72181"
FT BINDING 232
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000250|UniProtKB:P72181"
FT BINDING 245
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000250|UniProtKB:P72181"
FT BINDING 272
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000250|UniProtKB:P72181"
FT BINDING 292
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000250|UniProtKB:P72181"
FT BINDING 420
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000250|UniProtKB:P72181"
FT BINDING 536
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000250|UniProtKB:P72181"
FT BINDING 583
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000250|UniProtKB:P72181"
SQ SEQUENCE 596 AA; 65440 MW; 90C981B688A74BD3 CRC64;
MRQRTPFARP GLLASAALAL VLGPLAVAAQ EQAAPPKDPA AALEDHKTKT DNRYEPSLDN
LAQQDVAALG APEGIPALSD AQYNEANKIY FERCAGCHGV LRKGATGKAL TPDLTRDLGF
DYLQSFITYG SPAGMPNWGT SGELTAEQVD LMANYLLLDP AAPPEFGMKE MRESWQVHVA
PEDRPTQQEN DWDLENLFSV TLRDAGQIAL IDGTTYEIKS VLDTGYAVHI SRMSASGRYL
FVIGRDGKVN MIDLWMKEPA TVAEIKIGSE ARSIETSKME GWEDKYAIAG AYWPPQYVIM
DGETLEPMKI QSTRGMIYDE QEYHPEPRVA AILASHYRPE FIVNVKETGK ILLVDYTDLK
NLKTTEIEAE RFLHDGGLDG SHRYFITAAN ARNKLVVIDT KEGKLVAIED TGGQTPHPGR
GANFVHPTFG PVWATSHMGD DSVALIGTDP EGHPDNAWKI LDSFPALGGG SLFIKTHPNS
QYLYVDATLN PEAEISGSVA VFDTKAMTGD GSDPEFKTLP IAEWAGIAEG QPRVVQGEFN
KDGTEVWFSV WNGKDQESAL VVVDDKTLEL KHVIKDERLV TPTGKFNVYN TMTDTY
