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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)DescriptionActionsGraphical viewLength
    Metal bindingi94Iron (heme 3 axial ligand)Combined sources1
    Binding sitei122Heme 1 (covalent)Combined sources1
    Binding sitei125Heme 1 (covalent)Combined sources1
    Metal bindingi126Iron (heme 1 axial ligand)Combined sources1
    Binding sitei160Heme 2 (covalent)Combined sources1
    Binding sitei163Heme 2 (covalent)Combined sources1
    Metal bindingi164Iron (heme 2 axial ligand)Combined sources1
    Binding sitei209Heme 3 (covalent)Combined sources1
    Binding sitei212Heme 3 (covalent)Combined sources1
    Metal bindingi213Iron (heme 3 axial ligand)Combined sources1
    Metal bindingi215CalciumCombined sources1
    Metal bindingi216Calcium; via carbonyl oxygenCombined sources1
    Binding sitei216SubstrateCurated1
    Metal bindingi261Calcium; via carbonyl oxygenCombined sources1
    Metal bindingi263CalciumCombined sources1
    Binding sitei264SubstrateCurated1
    Metal bindingi275Iron (heme 5 axial ligand)Combined sources1
    Binding sitei282Heme 4 (covalent)Combined sources1
    Binding sitei285Heme 4 (covalent)Combined sources1
    Metal bindingi286Iron (heme 4 axial ligand)Combined sources1
    Metal bindingi301Iron (heme 2 axial ligand)Combined sources1
    Binding sitei314Heme 5 (covalent)Combined sources1
    Binding sitei317Heme 5 (covalent)Combined sources1
    Metal bindingi318Iron (heme 5 axial ligand)Combined sources1
    Metal bindingi393Iron (heme 4 axial ligand)Combined sources1

    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    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)DescriptionActionsGraphical viewLength
    Mutagenesisi126K → H, I or L: Almost complete loss of nitrite reductase activity. 1 Publication1
    Mutagenesisi263Q → E: Increases affinity for nitrite without changing Vmax. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Signal peptidei1 – 261 PublicationAdd BLAST26
    ChainiPRO_000000657827 – 478Cytochrome c-552Add BLAST452

    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 interactors.
    DIPiDIP-36021N.
    IntActiP0ABK9. 3 interactors.
    STRINGi511145.b4070.

    Structurei

    Secondary structure

    1478
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi42 – 45Combined sources4
    Turni46 – 48Combined sources3
    Helixi50 – 57Combined sources8
    Helixi58 – 61Combined sources4
    Helixi68 – 71Combined sources4
    Helixi74 – 78Combined sources5
    Turni79 – 81Combined sources3
    Helixi83 – 85Combined sources3
    Helixi94 – 96Combined sources3
    Helixi97 – 103Combined sources7
    Helixi105 – 107Combined sources3
    Beta strandi116 – 119Combined sources4
    Helixi120 – 123Combined sources4
    Turni124 – 126Combined sources3
    Helixi129 – 137Combined sources9
    Helixi139 – 143Combined sources5
    Beta strandi144 – 146Combined sources3
    Helixi147 – 150Combined sources4
    Turni151 – 153Combined sources3
    Helixi160 – 163Combined sources4
    Helixi169 – 172Combined sources4
    Helixi183 – 191Combined sources9
    Helixi196 – 198Combined sources3
    Helixi201 – 209Combined sources9
    Turni210 – 212Combined sources3
    Beta strandi217 – 219Combined sources3
    Turni220 – 223Combined sources4
    Beta strandi224 – 226Combined sources3
    Helixi235 – 244Combined sources10
    Beta strandi249 – 251Combined sources3
    Turni253 – 255Combined sources3
    Helixi266 – 272Combined sources7
    Helixi274 – 277Combined sources4
    Helixi282 – 286Combined sources5
    Beta strandi289 – 291Combined sources3
    Beta strandi297 – 299Combined sources3
    Helixi306 – 312Combined sources7
    Helixi314 – 316Combined sources3
    Helixi322 – 359Combined sources38
    Helixi364 – 385Combined sources22
    Helixi390 – 393Combined sources4
    Helixi395 – 422Combined sources28
    Helixi437 – 443Combined sources7
    Helixi448 – 472Combined sources25

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB 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.
    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
    PDB 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.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4259405. 10 interactors.
    DIPiDIP-36021N.
    IntActiP0ABK9. 3 interactors.
    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: November 2, 2016
    This is version 97 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.