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 24-JAN-2024, entry version 131. 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; Pseudomonadota; Alphaproteobacteria; Rhodobacterales; OC Paracoccaceae; 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. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- 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; 82367.SAMN04244567_00716; -. DR DrugBank; DB03317; Ferroheme C. DR DrugBank; DB03469; Heme D. DR DrugBank; DB03309; N-cyclohexyltaurine. DR GeneID; 51371260; -. DR eggNOG; COG2010; Bacteria. DR OrthoDB; 5290932at2; -. 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; 2.140.10.20; C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase; 1. DR Gene3D; 1.10.760.10; Cytochrome c-like domain; 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; PF02239; Cytochrom_D1; 1. DR Pfam; PF13442; Cytochrome_CBB3; 1. DR SUPFAM; SSF51004; C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase; 1. DR SUPFAM; SSF46626; Cytochrome c; 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 //