NIRS_PARPN
ID NIRS_PARPN Reviewed; 596 AA.
AC P72181; Q9FCQ0;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 08-NOV-2002, sequence version 2.
DT 03-AUG-2022, entry version 126.
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;
OS Paracoccus pantotrophus (Thiosphaera pantotropha).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC Rhodobacteraceae; Paracoccus.
OX NCBI_TaxID=82367;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=LMD 92.63;
RX PubMed=10708389; DOI=10.1099/00221287-146-2-509;
RA Saunders N.F.W., Ferguson S.J., Baker S.C.;
RT "Transcriptional analysis of the nirS gene, encoding cytochrome cd1 nitrite
RT reductase, of Paracoccus pantotrophus LMD 92.63.";
RL Microbiology 146:509-516(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=11237728; DOI=10.1006/bbrc.2001.4425;
RA Gordon E.H.J., Steensma E., Ferguson S.J.;
RT "The cytochrome c domain of dimeric cytochrome cd(1) of Paracoccus
RT pantotrophus can be produced at high levels as a monomeric holoprotein
RT using an improved c-type cytochrome expression system in Escherichia
RT coli.";
RL Biochem. Biophys. Res. Commun. 281:788-794(2001).
RN [3] {ECO:0007744|PDB:1QKS}
RP X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) OF 30-596 IN COMPLEX WITH HEME C AND
RP HEME D1, AND COFACTOR.
RX PubMed=7736589; DOI=10.1016/0092-8674(95)90390-9;
RA Fueloep V., Moir J.W.B., Ferguson S.J., Hajdu J.;
RT "The anatomy of a bifunctional enzyme: structural basis for reduction of
RT oxygen to water and synthesis of nitric oxide by cytochrome cd1.";
RL Cell 81:369-377(1995).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.2 ANGSTROMS).
RX PubMed=9199411; DOI=10.1006/jmbi.1997.1070;
RA Baker S.C., Saunders N.F.W., Willis A.C., Ferguson S.J., Fueloep V.,
RA Hajdu J.;
RT "Cytochrome cd1 structure: unusual haem environments in a nitrite reductase
RT and analysis of factors contributing to beta-propeller folds.";
RL J. Mol. Biol. 269:440-455(1997).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
RX PubMed=9311786; DOI=10.1038/38775;
RA Williams P.A., Fueloep V., Garman E.F., Saunders N.F.W., Ferguson S.J.,
RA Hajdu J.;
RT "Haem-ligand switching during catalysis in crystals of a nitrogen-cycle
RT enzyme.";
RL Nature 389:406-412(1997).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS).
RX PubMed=10998233; DOI=10.1021/bi000179q;
RA Sjoegren T., Svensson-Ek M., Hajdu J., Brzezinski P.;
RT "Proton-coupled structural changes upon binding of carbon monoxide to
RT cytochrome cd1: a combined flash photolysis and X-ray crystallography
RT study.";
RL Biochemistry 39:10967-10974(2000).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (1.59 ANGSTROMS).
RX PubMed=10827177; DOI=10.1074/jbc.m001377200;
RA Jafferji A., Allen J.W.A., Ferguson S.J., Fueloep V.;
RT "X-ray crystallographic study of cyanide binding provides insights into the
RT structure-function relationship for cytochrome cd1 nitrite reductase from
RT Paracoccus pantotrophus.";
RL J. Biol. Chem. 275:25089-25094(2000).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.46 ANGSTROMS).
RX PubMed=11278884; DOI=10.1074/jbc.m011312200;
RA Sjoegren T., Hajdu J.;
RT "Structure of the bound dioxygen species in the cytochrome oxidase reaction
RT of cytochrome cd1 nitrite reductase.";
RL J. Biol. Chem. 276:13072-13076(2001).
RN [9]
RP X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS).
RX PubMed=11373294; DOI=10.1074/jbc.m103657200;
RA Sjoegren T., Hajdu J.;
RT "The structure of an alternative form of Paracoccus pantotrophus cytochrome
RT cd1 nitrite reductase.";
RL J. Biol. Chem. 276:29450-29455(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 -!- 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:0000269|PubMed:7736589};
CC Note=Binds 1 heme c group covalently per subunit.
CC {ECO:0000269|PubMed:7736589};
CC -!- COFACTOR:
CC Name=heme; Xref=ChEBI:CHEBI:30413;
CC Evidence={ECO:0000269|PubMed:7736589};
CC Note=Binds 1 heme d1 group per subunit. {ECO:0000269|PubMed:7736589};
CC -!- SUBUNIT: Homodimer.
CC -!- SUBCELLULAR LOCATION: Periplasm.
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DR EMBL; U75413; AAB17878.1; -; Genomic_DNA.
DR EMBL; AJ401462; CAC03621.1; -; Genomic_DNA.
DR RefSeq; WP_024843009.1; NZ_RIAQ01000012.1.
DR PDB; 1AOF; X-ray; 2.00 A; A/B=30-596.
DR PDB; 1AOM; X-ray; 1.80 A; A/B=30-596.
DR PDB; 1AOQ; X-ray; 1.80 A; A/B=30-596.
DR PDB; 1DY7; X-ray; 1.60 A; A/B=30-596.
DR PDB; 1E2R; X-ray; 1.59 A; A/B=30-596.
DR PDB; 1GQ1; X-ray; 1.40 A; A/B=30-596.
DR PDB; 1H9X; X-ray; 2.10 A; A/B=30-596.
DR PDB; 1H9Y; X-ray; 2.40 A; A/B=30-596.
DR PDB; 1HCM; X-ray; 2.50 A; A/B=30-596.
DR PDB; 1HJ3; X-ray; 1.60 A; A/B=30-596.
DR PDB; 1HJ4; X-ray; 1.60 A; A/B=30-596.
DR PDB; 1HJ5; X-ray; 1.46 A; A/B=30-596.
DR PDB; 1QKS; X-ray; 1.28 A; A/B=30-596.
DR PDBsum; 1AOF; -.
DR PDBsum; 1AOM; -.
DR PDBsum; 1AOQ; -.
DR PDBsum; 1DY7; -.
DR PDBsum; 1E2R; -.
DR PDBsum; 1GQ1; -.
DR PDBsum; 1H9X; -.
DR PDBsum; 1H9Y; -.
DR PDBsum; 1HCM; -.
DR PDBsum; 1HJ3; -.
DR PDBsum; 1HJ4; -.
DR PDBsum; 1HJ5; -.
DR PDBsum; 1QKS; -.
DR AlphaFoldDB; P72181; -.
DR SMR; P72181; -.
DR STRING; 935565.JAEM01000004_gene3094; -.
DR DrugBank; DB03317; Ferroheme C.
DR DrugBank; DB03469; Heme D.
DR DrugBank; DB03309; N-cyclohexyltaurine.
DR eggNOG; COG2010; Bacteria.
DR BRENDA; 1.7.2.1; 4531.
DR EvolutionaryTrace; P72181; -.
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 1: Evidence at protein level;
KW 3D-structure; Electron transport; Heme; Iron; Metal-binding;
KW Oxidoreductase; Periplasm; Signal; Transport.
FT SIGNAL 1..29
FT CHAIN 30..596
FT /note="Nitrite reductase"
FT /id="PRO_0000006575"
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:0000269|PubMed:7736589,
FT ECO:0007744|PDB:1QKS"
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:0000269|PubMed:7736589,
FT ECO:0007744|PDB:1QKS"
FT BINDING 57
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000269|PubMed:7736589,
FT ECO:0007744|PDB:1QKS"
FT BINDING 94
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /note="covalent"
FT /evidence="ECO:0000269|PubMed:7736589,
FT ECO:0007744|PDB:1QKS"
FT BINDING 97
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /note="covalent"
FT /evidence="ECO:0000269|PubMed:7736589,
FT ECO:0007744|PDB:1QKS"
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:0000269|PubMed:7736589,
FT ECO:0007744|PDB:1QKS"
FT BINDING 108
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /evidence="ECO:0000269|PubMed:7736589,
FT ECO:0007744|PDB:1QKS"
FT BINDING 122
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /evidence="ECO:0000269|PubMed:7736589,
FT ECO:0007744|PDB:1QKS"
FT BINDING 138
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000269|PubMed:7736589,
FT ECO:0007744|PDB:1QKS"
FT BINDING 203
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000269|PubMed:7736589,
FT ECO:0007744|PDB:1QKS"
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:0000269|PubMed:7736589,
FT ECO:0007744|PDB:1QKS"
FT BINDING 232
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000269|PubMed:7736589,
FT ECO:0007744|PDB:1QKS"
FT BINDING 245
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000269|PubMed:7736589,
FT ECO:0007744|PDB:1QKS"
FT BINDING 272
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000269|PubMed:7736589,
FT ECO:0007744|PDB:1QKS"
FT BINDING 292
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000269|PubMed:7736589,
FT ECO:0007744|PDB:1QKS"
FT BINDING 420
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000269|PubMed:7736589,
FT ECO:0007744|PDB:1QKS"
FT BINDING 536
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000269|PubMed:7736589,
FT ECO:0007744|PDB:1QKS"
FT BINDING 583
FT /ligand="heme d1"
FT /ligand_id="ChEBI:CHEBI:60549"
FT /evidence="ECO:0000269|PubMed:7736589,
FT ECO:0007744|PDB:1QKS"
FT CONFLICT 28
FT /note="S -> A (in Ref. 1; AAB17878)"
FT /evidence="ECO:0000305"
FT CONFLICT 76
FT /note="S -> T (in Ref. 1; AAB17878)"
FT /evidence="ECO:0000305"
FT CONFLICT 130
FT /note="G -> A (in Ref. 1; AAB17878)"
FT /evidence="ECO:0000305"
FT CONFLICT 214
FT /note="A -> T (in Ref. 1; AAB17878)"
FT /evidence="ECO:0000305"
FT HELIX 39..41
FT /evidence="ECO:0007829|PDB:1QKS"
FT HELIX 42..45
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 50..55
FT /evidence="ECO:0007829|PDB:1HJ3"
FT HELIX 61..63
FT /evidence="ECO:0007829|PDB:1QKS"
FT HELIX 80..93
FT /evidence="ECO:0007829|PDB:1QKS"
FT HELIX 95..98
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 105..107
FT /evidence="ECO:0007829|PDB:1QKS"
FT HELIX 112..118
FT /evidence="ECO:0007829|PDB:1QKS"
FT HELIX 120..127
FT /evidence="ECO:0007829|PDB:1QKS"
FT TURN 132..134
FT /evidence="ECO:0007829|PDB:1DY7"
FT TURN 136..138
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 142..144
FT /evidence="ECO:0007829|PDB:1E2R"
FT HELIX 146..157
FT /evidence="ECO:0007829|PDB:1QKS"
FT HELIX 168..174
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 176..179
FT /evidence="ECO:0007829|PDB:1QKS"
FT HELIX 181..183
FT /evidence="ECO:0007829|PDB:1QKS"
FT HELIX 194..196
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 197..202
FT /evidence="ECO:0007829|PDB:1QKS"
FT TURN 203..206
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 207..212
FT /evidence="ECO:0007829|PDB:1QKS"
FT TURN 213..215
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 218..223
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 228..233
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 239..244
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 247..253
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 256..258
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 261..266
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 269..276
FT /evidence="ECO:0007829|PDB:1QKS"
FT TURN 283..285
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 286..293
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 296..301
FT /evidence="ECO:0007829|PDB:1QKS"
FT TURN 302..304
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 307..312
FT /evidence="ECO:0007829|PDB:1QKS"
FT TURN 318..320
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 323..325
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 329..334
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 336..345
FT /evidence="ECO:0007829|PDB:1QKS"
FT TURN 346..349
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 350..355
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 359..368
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 371..378
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 384..389
FT /evidence="ECO:0007829|PDB:1QKS"
FT HELIX 390..392
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 394..399
FT /evidence="ECO:0007829|PDB:1QKS"
FT TURN 400..403
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 404..410
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 412..416
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 422..426
FT /evidence="ECO:0007829|PDB:1QKS"
FT TURN 427..429
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 430..447
FT /evidence="ECO:0007829|PDB:1QKS"
FT TURN 450..452
FT /evidence="ECO:0007829|PDB:1QKS"
FT TURN 454..456
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 459..465
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 481..486
FT /evidence="ECO:0007829|PDB:1QKS"
FT HELIX 493..496
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 499..503
FT /evidence="ECO:0007829|PDB:1QKS"
FT HELIX 504..506
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 510..512
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 516..519
FT /evidence="ECO:0007829|PDB:1QKS"
FT HELIX 521..525
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 533..539
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 543..551
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 559..564
FT /evidence="ECO:0007829|PDB:1QKS"
FT TURN 565..568
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 569..574
FT /evidence="ECO:0007829|PDB:1QKS"
FT STRAND 581..587
FT /evidence="ECO:0007829|PDB:1QKS"
FT HELIX 588..592
FT /evidence="ECO:0007829|PDB:1QKS"
SQ SEQUENCE 596 AA; 65383 MW; ABAD0C871E8FB7F1 CRC64;
MRQRTPFARP GLLASAALAL VLGPLAASAQ EQVAPPKDPA AALEDHKTRT DNRYEPSLDN
LAQQDVAAPG APEGVSALSD AQYNEANKIY FERCAGCHGV LRKGATGKAL TPDLTRDLGF
DYLQSFITYG SPAGMPNWGT SGELSAEQVD LMANYLLLDP AAPPEFGMKE MRESWKVHVA
PEDRPTQQEN DWDLENLFSV TLRDAGQIAL IDGATYEIKS VLDTGYAVHI SRLSASGRYL
FVIGRDGKVN MIDLWMKEPT TVAEIKIGSE ARSIETSKME GWEDKYAIAG AYWPPQYVIM
DGETLEPKKI QSTRGMTYDE QEYHPEPRVA AILASHYRPE FIVNVKETGK ILLVDYTDLD
NLKTTEISAE RFLHDGGLDG SHRYFITAAN ARNKLVVIDT KEGKLVAIED TGGQTPHPGR
GANFVHPTFG PVWATSHMGD DSVALIGTDP EGHPDNAWKI LDSFPALGGG SLFIKTHPNS
QYLYVDATLN PEAEISGSVA VFDIKAMTGD GSDPEFKTLP IAEWAGITEG QPRVVQGEFN
KDGTEVWFSV WNGKDQESAL VVVDDKTLEL KHVIKDERLV TPTGKFNVYN TMTDTY
