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Protein

Cytochrome c-552

Gene

nrfA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the reduction of nitrite to ammonia, consuming six electrons in the process (PubMed:9593308, PubMed:11863430, PubMed:18311941, PubMed:20629638). Has very low activity toward hydroxylamine (PubMed:11863430). Has even lower activity toward sulfite (PubMed:20629638). Sulfite reductase activity is maximal at neutral pH (By similarity).By similarity1 Publication4 Publications

Catalytic activityi

NH3 + 2 H2O + 6 ferricytochrome c = nitrite + 6 ferrocytochrome c + 7 H+.4 Publications

Cofactori

Protein has several cofactor binding sites:

Enzyme regulationi

Subject to competitive inhibition by sulfite.1 Publication

Kineticsi

  1. KM=28 µM for nitrite1 Publication
  2. KM=30 µM for nitrite1 Publication
  3. KM=22 µM for nitrite1 Publication
  4. KM=70 µM for sulfite1 Publication
  5. KM=30 mM for hydroxylamine1 Publication

    Pathwayi: nitrate reduction (assimilation)

    This protein is involved in the pathway nitrate reduction (assimilation), which is part of Nitrogen metabolism.1 Publication
    View all proteins of this organism that are known to be involved in the pathway nitrate reduction (assimilation) and in Nitrogen metabolism.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi94 – 941Iron (heme 3 axial ligand)Combined sources
    Binding sitei122 – 1221Heme 1 (covalent)Combined sources
    Binding sitei125 – 1251Heme 1 (covalent)Combined sources
    Metal bindingi126 – 1261Iron (heme 1 axial ligand)Combined sources
    Binding sitei160 – 1601Heme 2 (covalent)Combined sources
    Binding sitei163 – 1631Heme 2 (covalent)Combined sources
    Metal bindingi164 – 1641Iron (heme 2 axial ligand)Combined sources
    Binding sitei209 – 2091Heme 3 (covalent)Combined sources
    Binding sitei212 – 2121Heme 3 (covalent)Combined sources
    Metal bindingi213 – 2131Iron (heme 3 axial ligand)Combined sources
    Metal bindingi215 – 2151CalciumCombined sources
    Metal bindingi216 – 2161Calcium; via carbonyl oxygenCombined sources
    Binding sitei216 – 2161SubstrateCurated
    Metal bindingi261 – 2611Calcium; via carbonyl oxygenCombined sources
    Metal bindingi263 – 2631CalciumCombined sources
    Binding sitei264 – 2641SubstrateCurated
    Metal bindingi275 – 2751Iron (heme 5 axial ligand)Combined sources
    Binding sitei282 – 2821Heme 4 (covalent)Combined sources
    Binding sitei285 – 2851Heme 4 (covalent)Combined sources
    Metal bindingi286 – 2861Iron (heme 4 axial ligand)Combined sources
    Metal bindingi301 – 3011Iron (heme 2 axial ligand)Combined sources
    Binding sitei314 – 3141Heme 5 (covalent)Combined sources
    Binding sitei317 – 3171Heme 5 (covalent)Combined sources
    Metal bindingi318 – 3181Iron (heme 5 axial ligand)Combined sources
    Metal bindingi393 – 3931Iron (heme 4 axial ligand)Combined sources

    GO - Molecular functioni

    • calcium ion binding Source: UniProtKB-HAMAP
    • heme binding Source: EcoCyc
    • iron ion binding Source: UniProtKB-HAMAP
    • nitric oxide reductase activity Source: CACAO
    • nitrite reductase (cytochrome, ammonia-forming) activity Source: EcoCyc

    GO - Biological processi

    • anaerobic electron transport chain Source: EcoCyc
    • nitrate assimilation Source: UniProtKB-UniPathway
    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Electron transport, Transport

    Keywords - Ligandi

    Calcium, Heme, Iron, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:CYTOCHROMEC552-MONOMER.
    ECOL316407:JW4031-MONOMER.
    MetaCyc:CYTOCHROMEC552-MONOMER.
    BRENDAi1.7.2.2. 2026.
    UniPathwayiUPA00653.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Cytochrome c-5521 Publication (EC:1.7.2.24 Publications)
    Alternative name(s):
    Ammonia-forming cytochrome c nitrite reductase
    Short name:
    Cytochrome c nitrite reductase1 Publication
    Gene namesi
    Name:nrfA
    Ordered Locus Names:b4070, JW4031
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11781. nrfA.

    Subcellular locationi

    GO - Cellular componenti

    • outer membrane-bounded periplasmic space Source: EcoCyc
    Complete GO annotation...

    Keywords - Cellular componenti

    Periplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi126 – 1261K → H, I or L: Almost complete loss of nitrite reductase activity. 1 Publication
    Mutagenesisi263 – 2631Q → E: Increases affinity for nitrite without changing Vmax. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Signal peptidei1 – 26261 PublicationAdd
    BLAST
    Chaini27 – 478452Cytochrome c-552PRO_0000006578Add
    BLAST

    Proteomic databases

    PaxDbiP0ABK9.
    PRIDEiP0ABK9.

    Expressioni

    Inductioni

    Full induction attained in the presence of nitrite. Subject to glucose and nitrate repression.1 Publication

    Interactioni

    Subunit structurei

    Homodimer (PubMed:11863430, PubMed:18311941). Component of a membrane-associated heterooligomeric complex (Probable).Curated2 Publications

    Protein-protein interaction databases

    BioGridi4259405. 10 interactions.
    DIPiDIP-36021N.
    IntActiP0ABK9. 3 interactions.
    STRINGi511145.b4070.

    Structurei

    Secondary structure

    1
    478
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi42 – 454Combined sources
    Turni46 – 483Combined sources
    Helixi50 – 578Combined sources
    Helixi58 – 614Combined sources
    Helixi68 – 714Combined sources
    Helixi74 – 785Combined sources
    Turni79 – 813Combined sources
    Helixi83 – 853Combined sources
    Helixi94 – 963Combined sources
    Helixi97 – 1037Combined sources
    Helixi105 – 1073Combined sources
    Beta strandi116 – 1194Combined sources
    Helixi120 – 1234Combined sources
    Turni124 – 1263Combined sources
    Helixi129 – 1379Combined sources
    Helixi139 – 1435Combined sources
    Beta strandi144 – 1463Combined sources
    Helixi147 – 1504Combined sources
    Turni151 – 1533Combined sources
    Helixi160 – 1634Combined sources
    Helixi169 – 1724Combined sources
    Helixi183 – 1919Combined sources
    Helixi196 – 1983Combined sources
    Helixi201 – 2099Combined sources
    Turni210 – 2123Combined sources
    Beta strandi217 – 2193Combined sources
    Turni220 – 2234Combined sources
    Beta strandi224 – 2263Combined sources
    Helixi235 – 24410Combined sources
    Beta strandi249 – 2513Combined sources
    Turni253 – 2553Combined sources
    Helixi266 – 2727Combined sources
    Helixi274 – 2774Combined sources
    Helixi282 – 2865Combined sources
    Beta strandi289 – 2913Combined sources
    Beta strandi297 – 2993Combined sources
    Helixi306 – 3127Combined sources
    Helixi314 – 3163Combined sources
    Helixi322 – 35938Combined sources
    Helixi364 – 38522Combined sources
    Helixi390 – 3934Combined sources
    Helixi395 – 42228Combined sources
    Helixi437 – 4437Combined sources
    Helixi448 – 47225Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1GU6X-ray2.50A/C/E/G27-478[»]
    2RDZX-ray1.74A/B/C/D27-478[»]
    2RF7X-ray2.04A/B/C/D37-477[»]
    3L1TX-ray2.30A/B/C/D27-478[»]
    3TORX-ray2.00A/B/C/D27-478[»]
    4WJYX-ray2.15A/B27-478[»]
    ProteinModelPortaliP0ABK9.
    SMRiP0ABK9. Positions 37-477.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0ABK9.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the cytochrome c-552 family.Curated

    Keywords - Domaini

    Signal

    Phylogenomic databases

    eggNOGiENOG4105EAU. Bacteria.
    COG3303. LUCA.
    HOGENOMiHOG000278511.
    InParanoidiP0ABK9.
    KOiK03385.
    OMAiCHEKGKS.
    PhylomeDBiP0ABK9.

    Family and domain databases

    Gene3Di1.10.710.10. 1 hit.
    HAMAPiMF_01182. Cytochrom_C552. 1 hit.
    InterProiIPR023155. Cyt_c-552/4.
    IPR003321. Cyt_c552.
    IPR017570. Cyt_c_NO2Rdtase_formate-dep.
    IPR011031. Multihaem_cyt.
    [Graphical view]
    PfamiPF02335. Cytochrom_C552. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000243. Cyt_c552. 1 hit.
    SUPFAMiSSF48695. SSF48695. 1 hit.
    TIGRFAMsiTIGR03152. cyto_c552_HCOOH. 1 hit.
    PROSITEiPS51008. MULTIHEME_CYTC. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    P0ABK9-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MTRIKINARR IFSLLIPFFF FTSVHAEQTA APAKPVTVEA KNETFAPQHP
    60 70 80 90 100
    DQYLSWKATS EQSERVDALA EDPRLVILWA GYPFSRDYNK PRGHAFAVTD
    110 120 130 140 150
    VRETLRTGAP KNAEDGPLPM ACWSCKSPDV ARLIQKDGED GYFHGKWARG
    160 170 180 190 200
    GPEIVNNLGC ADCHNTASPE FAKGKPELTL SRPYAARAME AIGKPFEKAG
    210 220 230 240 250
    RFDQQSMVCG QCHVEYYFDG KNKAVKFPWD DGMKVENMEQ YYDKIAFSDW
    260 270 280 290 300
    TNSLSKTPML KAQHPEYETW TAGIHGKNNV TCIDCHMPKV QNAEGKLYTD
    310 320 330 340 350
    HKIGNPFDNF AQTCANCHTQ DKAALQKVVA ERKQSINDLK IKVEDQLVHA
    360 370 380 390 400
    HFEAKAALDA GATEAEMKPI QDDIRHAQWR WDLAIASHGI HMHAPEEGLR
    410 420 430 440 450
    MLGTAMDKAA DARTKLARLL ATKGITHEIQ IPDISTKEKA QQAIGLNMEQ
    460 470
    IKAEKQDFIK TVIPQWEEQA RKNGLLSQ
    Length:478
    Mass (Da):53,703
    Last modified:November 8, 2005 - v1
    Checksum:iF965E986412A0456
    GO

    Mass spectrometryi

    Molecular mass is 53590 Da from positions 27 - 478. Determined by MALDI. 1 Publication

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X72298 Genomic DNA. Translation: CAA51048.1.
    U00006 Genomic DNA. Translation: AAC43164.1.
    U00096 Genomic DNA. Translation: AAC77040.1.
    AP009048 Genomic DNA. Translation: BAE78072.1.
    PIRiS39590.
    RefSeqiNP_418494.1. NC_000913.3.
    WP_000196875.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC77040; AAC77040; b4070.
    BAE78072; BAE78072; BAE78072.
    GeneIDi948571.
    KEGGiecj:JW4031.
    eco:b4070.
    PATRICi32123689. VBIEscCol129921_4193.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X72298 Genomic DNA. Translation: CAA51048.1.
    U00006 Genomic DNA. Translation: AAC43164.1.
    U00096 Genomic DNA. Translation: AAC77040.1.
    AP009048 Genomic DNA. Translation: BAE78072.1.
    PIRiS39590.
    RefSeqiNP_418494.1. NC_000913.3.
    WP_000196875.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1GU6X-ray2.50A/C/E/G27-478[»]
    2RDZX-ray1.74A/B/C/D27-478[»]
    2RF7X-ray2.04A/B/C/D37-477[»]
    3L1TX-ray2.30A/B/C/D27-478[»]
    3TORX-ray2.00A/B/C/D27-478[»]
    4WJYX-ray2.15A/B27-478[»]
    ProteinModelPortaliP0ABK9.
    SMRiP0ABK9. Positions 37-477.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4259405. 10 interactions.
    DIPiDIP-36021N.
    IntActiP0ABK9. 3 interactions.
    STRINGi511145.b4070.

    Proteomic databases

    PaxDbiP0ABK9.
    PRIDEiP0ABK9.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC77040; AAC77040; b4070.
    BAE78072; BAE78072; BAE78072.
    GeneIDi948571.
    KEGGiecj:JW4031.
    eco:b4070.
    PATRICi32123689. VBIEscCol129921_4193.

    Organism-specific databases

    EchoBASEiEB1729.
    EcoGeneiEG11781. nrfA.

    Phylogenomic databases

    eggNOGiENOG4105EAU. Bacteria.
    COG3303. LUCA.
    HOGENOMiHOG000278511.
    InParanoidiP0ABK9.
    KOiK03385.
    OMAiCHEKGKS.
    PhylomeDBiP0ABK9.

    Enzyme and pathway databases

    UniPathwayiUPA00653.
    BioCyciEcoCyc:CYTOCHROMEC552-MONOMER.
    ECOL316407:JW4031-MONOMER.
    MetaCyc:CYTOCHROMEC552-MONOMER.
    BRENDAi1.7.2.2. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP0ABK9.
    PROiP0ABK9.

    Family and domain databases

    Gene3Di1.10.710.10. 1 hit.
    HAMAPiMF_01182. Cytochrom_C552. 1 hit.
    InterProiIPR023155. Cyt_c-552/4.
    IPR003321. Cyt_c552.
    IPR017570. Cyt_c_NO2Rdtase_formate-dep.
    IPR011031. Multihaem_cyt.
    [Graphical view]
    PfamiPF02335. Cytochrom_C552. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000243. Cyt_c552. 1 hit.
    SUPFAMiSSF48695. SSF48695. 1 hit.
    TIGRFAMsiTIGR03152. cyto_c552_HCOOH. 1 hit.
    PROSITEiPS51008. MULTIHEME_CYTC. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiNRFA_ECOLI
    AccessioniPrimary (citable) accession number: P0ABK9
    Secondary accession number(s): P32050, Q2M6N4
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 8, 2005
    Last sequence update: November 8, 2005
    Last modified: September 7, 2016
    This is version 95 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.