NRFA_SHEON
ID NRFA_SHEON Reviewed; 467 AA.
AC Q8EAC7;
DT 12-DEC-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 121.
DE RecName: Full=Cytochrome c-552 {ECO:0000255|HAMAP-Rule:MF_01182};
DE EC=1.7.2.2 {ECO:0000255|HAMAP-Rule:MF_01182, ECO:0000269|PubMed:22382353};
DE AltName: Full=Ammonia-forming cytochrome c nitrite reductase {ECO:0000255|HAMAP-Rule:MF_01182};
DE Short=Cytochrome c nitrite reductase {ECO:0000255|HAMAP-Rule:MF_01182, ECO:0000303|PubMed:22382353};
DE Flags: Precursor;
GN Name=nrfA {ECO:0000255|HAMAP-Rule:MF_01182}; OrderedLocusNames=SO_3980;
OS Shewanella oneidensis (strain MR-1).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
OC Shewanellaceae; Shewanella.
OX NCBI_TaxID=211586;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MR-1;
RX PubMed=12368813; DOI=10.1038/nbt749;
RA Heidelberg J.F., Paulsen I.T., Nelson K.E., Gaidos E.J., Nelson W.C.,
RA Read T.D., Eisen J.A., Seshadri R., Ward N.L., Methe B.A., Clayton R.A.,
RA Meyer T., Tsapin A., Scott J., Beanan M.J., Brinkac L.M., Daugherty S.C.,
RA DeBoy R.T., Dodson R.J., Durkin A.S., Haft D.H., Kolonay J.F., Madupu R.,
RA Peterson J.D., Umayam L.A., White O., Wolf A.M., Vamathevan J.J.,
RA Weidman J.F., Impraim M., Lee K., Berry K.J., Lee C., Mueller J.,
RA Khouri H.M., Gill J., Utterback T.R., McDonald L.A., Feldblyum T.V.,
RA Smith H.O., Venter J.C., Nealson K.H., Fraser C.M.;
RT "Genome sequence of the dissimilatory metal ion-reducing bacterium
RT Shewanella oneidensis.";
RL Nat. Biotechnol. 20:1118-1123(2002).
RN [2] {ECO:0007744|PDB:3UBR}
RP X-RAY CRYSTALLOGRAPHY (2.59 ANGSTROMS) OF 28-466 IN COMPLEX WITH CALCIUM
RP AND HEME, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES,
RP COFACTOR, SUBCELLULAR LOCATION, AND PATHWAY.
RX PubMed=22382353; DOI=10.1007/s00775-012-0885-0;
RA Youngblut M., Judd E.T., Srajer V., Sayyed B., Goelzer T., Elliott S.J.,
RA Schmidt M., Pacheco A.A.;
RT "Laue crystal structure of Shewanella oneidensis cytochrome c nitrite
RT reductase from a high-yield expression system.";
RL J. Biol. Inorg. Chem. 17:647-662(2012).
CC -!- FUNCTION: Catalyzes the reduction of nitrite to ammonia, consuming six
CC electrons in the process (PubMed:22382353). Has very low activity
CC toward hydroxylamine (PubMed:22382353). Has even lower activity toward
CC sulfite. Sulfite reductase activity is maximal at neutral pH (By
CC similarity). {ECO:0000250|UniProtKB:L0DSL2,
CC ECO:0000269|PubMed:22382353}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=6 Fe(III)-[cytochrome c] + 2 H2O + NH4(+) = 6 Fe(II)-
CC [cytochrome c] + 8 H(+) + nitrite; Xref=Rhea:RHEA:13089, Rhea:RHEA-
CC COMP:10350, Rhea:RHEA-COMP:14399, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16301, ChEBI:CHEBI:28938,
CC ChEBI:CHEBI:29033, ChEBI:CHEBI:29034; EC=1.7.2.2;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01182,
CC ECO:0000269|PubMed:22382353};
CC -!- COFACTOR:
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01182};
CC Note=Binds 1 Ca(2+) ion per monomer. {ECO:0000255|HAMAP-Rule:MF_01182,
CC ECO:0000269|PubMed:22382353};
CC -!- COFACTOR:
CC Name=heme c; Xref=ChEBI:CHEBI:61717;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01182,
CC ECO:0000269|PubMed:22382353};
CC Note=Binds 5 heme c groups covalently per monomer. {ECO:0000255|HAMAP-
CC Rule:MF_01182, ECO:0000305|PubMed:22382353};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=23 uM for nitrite {ECO:0000269|PubMed:22382353};
CC KM=8300 uM for hydroxylamine {ECO:0000269|PubMed:22382353};
CC Note=kcat is 824 sec(-1) with nitrite as substrate. kcat is 2380
CC sec(-1) with hydroxylamine as substrate.
CC {ECO:0000269|PubMed:22382353};
CC -!- PATHWAY: Nitrogen metabolism; nitrate reduction (assimilation).
CC {ECO:0000255|HAMAP-Rule:MF_01182, ECO:0000305|PubMed:22382353}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:22382353}.
CC -!- SUBCELLULAR LOCATION: Periplasm {ECO:0000255|HAMAP-Rule:MF_01182,
CC ECO:0000305|PubMed:22382353}.
CC -!- SIMILARITY: Belongs to the cytochrome c-552 family. {ECO:0000255|HAMAP-
CC Rule:MF_01182}.
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DR EMBL; AE014299; AAN56954.1; -; Genomic_DNA.
DR RefSeq; NP_719510.1; NC_004347.2.
DR RefSeq; WP_011073711.1; NZ_CP053946.1.
DR PDB; 3UBR; X-ray; 2.59 A; A/B=28-466.
DR PDB; 6P73; X-ray; 1.65 A; A/B=28-466.
DR PDBsum; 3UBR; -.
DR PDBsum; 6P73; -.
DR AlphaFoldDB; Q8EAC7; -.
DR SMR; Q8EAC7; -.
DR STRING; 211586.SO_3980; -.
DR PaxDb; Q8EAC7; -.
DR KEGG; son:SO_3980; -.
DR PATRIC; fig|211586.12.peg.3862; -.
DR eggNOG; COG3303; Bacteria.
DR HOGENOM; CLU_035040_1_0_6; -.
DR OMA; EMVILWA; -.
DR OrthoDB; 738283at2; -.
DR PhylomeDB; Q8EAC7; -.
DR BioCyc; SONE211586:G1GMP-3689-MON; -.
DR BRENDA; 1.7.2.2; 5706.
DR SABIO-RK; Q8EAC7; -.
DR UniPathway; UPA00653; -.
DR Proteomes; UP000008186; Chromosome.
DR GO; GO:0030288; C:outer membrane-bounded periplasmic space; IBA:GO_Central.
DR GO; GO:0005509; F:calcium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0020037; F:heme binding; IBA:GO_Central.
DR GO; GO:0005506; F:iron ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0042279; F:nitrite reductase (cytochrome, ammonia-forming) activity; IBA:GO_Central.
DR GO; GO:0019645; P:anaerobic electron transport chain; IBA:GO_Central.
DR GO; GO:0042128; P:nitrate assimilation; IEA:UniProtKB-UniPathway.
DR CDD; cd00548; NrfA-like; 1.
DR HAMAP; MF_01182; Cytochrom_C552; 1.
DR InterPro; IPR003321; Cyt_c552.
DR InterPro; IPR017570; Cyt_c_NO2Rdtase_formate-dep.
DR InterPro; IPR036280; Multihaem_cyt_sf.
DR PANTHER; PTHR30633; PTHR30633; 1.
DR Pfam; PF02335; Cytochrom_C552; 1.
DR PIRSF; PIRSF000243; Cyt_c552; 1.
DR SUPFAM; SSF48695; SSF48695; 1.
DR TIGRFAMs; TIGR03152; cyto_c552_HCOOH; 1.
DR PROSITE; PS51008; MULTIHEME_CYTC; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Calcium; Electron transport; Heme; Iron; Metal-binding;
KW Oxidoreductase; Periplasm; Reference proteome; Signal; Transport.
FT SIGNAL 1..27
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182"
FT CHAIN 28..467
FT /note="Cytochrome c-552"
FT /id="PRO_0000268975"
FT BINDING 87
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="3"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182,
FT ECO:0007744|PDB:3UBR"
FT BINDING 115
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="1"
FT /note="covalent"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182,
FT ECO:0007744|PDB:3UBR"
FT BINDING 118
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="1"
FT /note="covalent"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182, ECO:0000305"
FT BINDING 119
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="1"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182,
FT ECO:0007744|PDB:3UBR"
FT BINDING 153
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="2"
FT /note="covalent"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182"
FT BINDING 156
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="2"
FT /note="covalent"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182"
FT BINDING 157
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="2"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182,
FT ECO:0007744|PDB:3UBR"
FT BINDING 195
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="3"
FT /note="covalent"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182,
FT ECO:0007744|PDB:3UBR"
FT BINDING 198
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="3"
FT /note="covalent"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182,
FT ECO:0007744|PDB:3UBR"
FT BINDING 199
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="3"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182,
FT ECO:0007744|PDB:3UBR"
FT BINDING 201
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182,
FT ECO:0007744|PDB:3UBR"
FT BINDING 202
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182,
FT ECO:0007744|PDB:3UBR"
FT BINDING 202
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182"
FT BINDING 250
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182,
FT ECO:0007744|PDB:3UBR"
FT BINDING 252
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182,
FT ECO:0007744|PDB:3UBR"
FT BINDING 253
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182"
FT BINDING 264
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="5"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182,
FT ECO:0007744|PDB:3UBR"
FT BINDING 271
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="4"
FT /note="covalent"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182,
FT ECO:0007744|PDB:3UBR"
FT BINDING 274
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="4"
FT /note="covalent"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182"
FT BINDING 275
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="4"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182,
FT ECO:0007744|PDB:3UBR"
FT BINDING 290
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="2"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182,
FT ECO:0007744|PDB:3UBR"
FT BINDING 303
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="5"
FT /note="covalent"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182,
FT ECO:0007744|PDB:3UBR"
FT BINDING 306
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="5"
FT /note="covalent"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182"
FT BINDING 307
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="5"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182,
FT ECO:0007744|PDB:3UBR"
FT BINDING 382
FT /ligand="heme c"
FT /ligand_id="ChEBI:CHEBI:61717"
FT /ligand_label="4"
FT /ligand_part="Fe"
FT /ligand_part_id="ChEBI:CHEBI:18248"
FT /note="axial binding residue"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01182,
FT ECO:0007744|PDB:3UBR"
FT TURN 35..41
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 43..50
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 51..54
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 61..64
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 67..71
FT /evidence="ECO:0007829|PDB:6P73"
FT TURN 72..74
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 76..78
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 87..89
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 90..96
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 98..100
FT /evidence="ECO:0007829|PDB:6P73"
FT STRAND 109..112
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 113..116
FT /evidence="ECO:0007829|PDB:6P73"
FT TURN 117..119
FT /evidence="ECO:0007829|PDB:3UBR"
FT HELIX 122..136
FT /evidence="ECO:0007829|PDB:6P73"
FT STRAND 137..139
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 140..143
FT /evidence="ECO:0007829|PDB:6P73"
FT TURN 144..146
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 153..156
FT /evidence="ECO:0007829|PDB:6P73"
FT STRAND 159..164
FT /evidence="ECO:0007829|PDB:3UBR"
FT HELIX 169..177
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 182..184
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 187..195
FT /evidence="ECO:0007829|PDB:6P73"
FT TURN 196..198
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 208..210
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 224..233
FT /evidence="ECO:0007829|PDB:6P73"
FT STRAND 238..240
FT /evidence="ECO:0007829|PDB:6P73"
FT TURN 242..244
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 255..259
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 263..266
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 271..275
FT /evidence="ECO:0007829|PDB:6P73"
FT STRAND 278..280
FT /evidence="ECO:0007829|PDB:6P73"
FT STRAND 286..288
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 295..298
FT /evidence="ECO:0007829|PDB:6P73"
FT TURN 299..302
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 303..305
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 311..348
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 353..374
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 379..382
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 384..411
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 426..432
FT /evidence="ECO:0007829|PDB:6P73"
FT HELIX 437..464
FT /evidence="ECO:0007829|PDB:6P73"
SQ SEQUENCE 467 AA; 52334 MW; 4BC976E90CDC48E0 CRC64;
MMKKMTGKTF ALSALVAASF MAAGAMASDK TEPRNEVYKD KFKNQYNSWH DTAKSEELVD
ALEQDPNMVI LWAGYAFAKD YKAPRGHMYA VTDVRNTLRT GAPKNAEDGP LPMACWSCKS
PDVPRLIEEQ GEDGYFKGKW AKGGPEVTNT IGCSDCHEKG SPKLRISRPY VDRALDAIGT
PFSKASKQDK ESMVCAQCHV EYYFEKKEDK KGFVKFPWDM GVTVDQMEVY YDGIEFSDWT
HALSKTPMLK AQHPEYETWK MGIHGKNNVS CVDCHMPKVT SPEGKKFTDH KVGNPFDRFE
ETCATCHSQT KEFLVGVTNE RKAKVKEMKL KAEEQLVKAH FEAAKAWELG ATEAEMKPIL
TDIRHAQWRW DLAIASHGVA AHAPEEALRV LGTSVNKAAD ARVKLAQLLA KKGLTDPVAI
PDISTKAKAQ AVLGMDMEKM NAEKEAFKKD MLPKWDAEAK KREATYK
