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P52647

- NIFJ_ECOLI

UniProt

P52647 - NIFJ_ECOLI

Protein

Probable pyruvate-flavodoxin oxidoreductase

Gene

ydbK

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 3 out of 5- Protein inferred from homologyi
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    • History
      Entry version 132 (01 Oct 2014)
      Sequence version 2 (01 Nov 1997)
      Previous versions | rss
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    Functioni

    Oxidoreductase required for the transfer of electrons from pyruvate to flavodoxin.Curated

    Catalytic activityi

    Pyruvate + CoA + oxidized flavodoxin = acetyl-CoA + CO2 + reduced flavodoxin.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Metal bindingi689 – 6891Iron-sulfur 1 (4Fe-4S)Sequence Analysis
    Metal bindingi692 – 6921Iron-sulfur 1 (4Fe-4S)Sequence Analysis
    Metal bindingi695 – 6951Iron-sulfur 1 (4Fe-4S)Sequence Analysis
    Metal bindingi699 – 6991Iron-sulfur 2 (4Fe-4S)Sequence Analysis
    Metal bindingi745 – 7451Iron-sulfur 2 (4Fe-4S)Sequence Analysis
    Metal bindingi748 – 7481Iron-sulfur 2 (4Fe-4S)Sequence Analysis
    Metal bindingi751 – 7511Iron-sulfur 2 (4Fe-4S)Sequence Analysis
    Metal bindingi755 – 7551Iron-sulfur 1 (4Fe-4S)Sequence Analysis

    GO - Molecular functioni

    1. 4 iron, 4 sulfur cluster binding Source: UniProtKB-KW
    2. iron ion binding Source: InterPro
    3. pyruvate-flavodoxin oxidoreductase activity Source: EcoCyc
    4. thiamine pyrophosphate binding Source: InterPro

    GO - Biological processi

    1. electron transport chain Source: InterPro
    2. response to oxidative stress Source: EcoCyc

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Electron transport, Transport

    Keywords - Ligandi

    4Fe-4S, Iron, Iron-sulfur, Metal-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:G6701-MONOMER.
    ECOL316407:JW1372-MONOMER.
    MetaCyc:G6701-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Probable pyruvate-flavodoxin oxidoreductase (EC:1.2.7.-)
    Gene namesi
    Name:ydbK
    Ordered Locus Names:b1378, JW1372
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG13183. ydbK.

    Pathology & Biotechi

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 11741174Probable pyruvate-flavodoxin oxidoreductasePRO_0000215557Add
    BLAST

    Proteomic databases

    PaxDbiP52647.
    PRIDEiP52647.

    Expressioni

    Gene expression databases

    GenevestigatoriP52647.

    Interactioni

    Protein-protein interaction databases

    DIPiDIP-11636N.
    IntActiP52647. 10 interactions.
    MINTiMINT-1299276.
    STRINGi511145.b1378.

    Structurei

    3D structure databases

    ProteinModelPortaliP52647.
    SMRiP52647. Positions 680-707, 740-771.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini680 – 709304Fe-4S ferredoxin-type 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini736 – 765304Fe-4S ferredoxin-type 2PROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

    Belongs to the NifJ family.Curated
    Contains 2 4Fe-4S ferredoxin-type domains.PROSITE-ProRule annotation

    Keywords - Domaini

    Repeat

    Phylogenomic databases

    eggNOGiCOG0674.
    HOGENOMiHOG000266425.
    KOiK03737.
    OMAiCVLAIFN.
    OrthoDBiEOG68H83G.
    PhylomeDBiP52647.

    Family and domain databases

    Gene3Di3.40.50.920. 1 hit.
    3.40.50.970. 2 hits.
    3.40.920.10. 1 hit.
    4.10.780.10. 1 hit.
    InterProiIPR001450. 4Fe4S-bd_dom.
    IPR017896. 4Fe4S_Fe-S-bd.
    IPR017900. 4Fe4S_Fe_S_CS.
    IPR019456. Pyrv-flavodox_OxRtase_EKR.
    IPR019752. Pyrv/ketoisovalerate_OxRed_cat.
    IPR002880. Pyrv_Fd/Flavodoxin_OxRdtase_N.
    IPR011895. Pyrv_flavodox_OxRed.
    IPR002869. Pyrv_flavodox_OxRed_cen.
    IPR029061. THDP-binding.
    IPR011766. TPP_enzyme-bd_C.
    IPR009014. Transketo_C/Pyr-ferredox_oxred.
    [Graphical view]
    PfamiPF10371. EKR. 1 hit.
    PF00037. Fer4. 2 hits.
    PF01558. POR. 1 hit.
    PF01855. POR_N. 1 hit.
    PF02775. TPP_enzyme_C. 1 hit.
    [Graphical view]
    PIRSFiPIRSF000159. NifJ. 1 hit.
    SMARTiSM00890. EKR. 1 hit.
    [Graphical view]
    SUPFAMiSSF52518. SSF52518. 2 hits.
    SSF52922. SSF52922. 1 hit.
    SSF53323. SSF53323. 1 hit.
    TIGRFAMsiTIGR02176. pyruv_ox_red. 1 hit.
    PROSITEiPS00198. 4FE4S_FER_1. 2 hits.
    PS51379. 4FE4S_FER_2. 2 hits.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P52647-1 [UniParc]FASTAAdd to Basket

    « Hide

    MITIDGNGAV ASVAFRTSEV IAIYPITPSS TMAEQADAWA GNGLKNVWGD     50
    TPRVVEMQSE AGAIATVHGA LQTGALSTSF TSSQGLLLMI PTLYKLAGEL 100
    TPFVLHVAAR TVATHALSIF GDHSDVMAVR QTGCAMLCAA NVQEAQDFAL 150
    ISQIATLKSR VPFIHFFDGF RTSHEINKIV PLADDTILDL MPQVEIDAHR 200
    ARALNPEHPV IRGTSANPDT YFQSREATNP WYNAVYDHVE QAMNDFSAAT 250
    GRQYQPFEYY GHPQAERVII LMGSAIGTCE EVVDELLTRG EKVGVLKVRL 300
    YRPFSAKHLL QALPGSVRSV AVLDRTKEPG AQAEPLYLDV MTALAEAFNN 350
    GERETLPRVI GGRYGLSSKE FGPDCVLAVF AELNAAKPKA RFTVGIYDDV 400
    TNLSLPLPEN TLPNSAKLEA LFYGLGSDGS VSATKNNIKI IGNSTPWYAQ 450
    GYFVYDSKKA GGLTVSHLRV SEQPIRSAYL ISQADFVGCH QLQFIDKYQM 500
    AERLKPGGIF LLNTPYSADE VWSRLPQEVQ AVLNQKKARF YVINAAKIAR 550
    ECGLAARINT VMQMAFFHLT QILPGDSALA ELQGAIAKSY SSKGQDLVER 600
    NWQALALARE SVEEVPLQPV NPHSANRPPV VSDAAPDFVK TVTAAMLAGL 650
    GDALPVSALP PDGTWPMGTT RWEKRNIAEE IPIWKEELCT QCNHCVAACP 700
    HSAIRAKVVP PEAMENAPAS LHSLDVKSRD MRGQKYVLQV APEDCTGCNL 750
    CVEVCPAKDR QNPEIKAINM MSRLEHVEEE KINYDFFLNL PEIDRSKLER 800
    IDIRTSQLIT PLFEYSGACS GCGETPYIKL LTQLYGDRML IANATGCSSI 850
    YGGNLPSTPY TTDANGRGPA WANSLFEDNA EFGLGFRLTV DQHRVRVLRL 900
    LDQFADKIPA ELLTALKSDA TPEVRREQVA ALRQQLNDVA EAHELLRDAD 950
    ALVEKSIWLI GGDGWAYDIG FGGLDHVLSL TENVNILVLD TQCYSNTGGQ 1000
    ASKATPLGAV TKFGEHGKRK ARKDLGVSMM MYGHVYVAQI SLGAQLNQTV 1050
    KAIQEAEAYP GPSLIIAYSP CEEHGYDLAL SHDQMRQLTA TGFWPLYRFD 1100
    PRRADEGKLP LALDSRPPSE APEETLLHEQ RFRRLNSQQP EVAEQLWKDA 1150
    AADLQKRYDF LAQMAGKAEK SNTD 1174
    Length:1,174
    Mass (Da):128,824
    Last modified:November 1, 1997 - v2
    Checksum:i2BBD1112285DC0F8
    GO

    Sequence cautioni

    The sequence U36928 differs from that shown. Reason: Frameshift at position 35.

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti40 – 401A → R(PubMed:9025293)Curated
    Sequence conflicti51 – 511T → S(PubMed:9025293)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U00096 Genomic DNA. Translation: AAC74460.1.
    AP009048 Genomic DNA. Translation: BAA14982.1.
    U36928 Genomic DNA. No translation available.
    PIRiE64888.
    RefSeqiNP_415896.1. NC_000913.3.
    YP_489646.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC74460; AAC74460; b1378.
    BAA14982; BAA14982; BAA14982.
    GeneIDi12932682.
    946587.
    KEGGiecj:Y75_p1354.
    eco:b1378.
    PATRICi32118040. VBIEscCol129921_1440.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U00096 Genomic DNA. Translation: AAC74460.1 .
    AP009048 Genomic DNA. Translation: BAA14982.1 .
    U36928 Genomic DNA. No translation available.
    PIRi E64888.
    RefSeqi NP_415896.1. NC_000913.3.
    YP_489646.1. NC_007779.1.

    3D structure databases

    ProteinModelPortali P52647.
    SMRi P52647. Positions 680-707, 740-771.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-11636N.
    IntActi P52647. 10 interactions.
    MINTi MINT-1299276.
    STRINGi 511145.b1378.

    Chemistry

    DrugBanki DB00698. Nitrofurantoin.

    Proteomic databases

    PaxDbi P52647.
    PRIDEi P52647.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC74460 ; AAC74460 ; b1378 .
    BAA14982 ; BAA14982 ; BAA14982 .
    GeneIDi 12932682.
    946587.
    KEGGi ecj:Y75_p1354.
    eco:b1378.
    PATRICi 32118040. VBIEscCol129921_1440.

    Organism-specific databases

    EchoBASEi EB2975.
    EcoGenei EG13183. ydbK.

    Phylogenomic databases

    eggNOGi COG0674.
    HOGENOMi HOG000266425.
    KOi K03737.
    OMAi CVLAIFN.
    OrthoDBi EOG68H83G.
    PhylomeDBi P52647.

    Enzyme and pathway databases

    BioCyci EcoCyc:G6701-MONOMER.
    ECOL316407:JW1372-MONOMER.
    MetaCyc:G6701-MONOMER.

    Miscellaneous databases

    PROi P52647.

    Gene expression databases

    Genevestigatori P52647.

    Family and domain databases

    Gene3Di 3.40.50.920. 1 hit.
    3.40.50.970. 2 hits.
    3.40.920.10. 1 hit.
    4.10.780.10. 1 hit.
    InterProi IPR001450. 4Fe4S-bd_dom.
    IPR017896. 4Fe4S_Fe-S-bd.
    IPR017900. 4Fe4S_Fe_S_CS.
    IPR019456. Pyrv-flavodox_OxRtase_EKR.
    IPR019752. Pyrv/ketoisovalerate_OxRed_cat.
    IPR002880. Pyrv_Fd/Flavodoxin_OxRdtase_N.
    IPR011895. Pyrv_flavodox_OxRed.
    IPR002869. Pyrv_flavodox_OxRed_cen.
    IPR029061. THDP-binding.
    IPR011766. TPP_enzyme-bd_C.
    IPR009014. Transketo_C/Pyr-ferredox_oxred.
    [Graphical view ]
    Pfami PF10371. EKR. 1 hit.
    PF00037. Fer4. 2 hits.
    PF01558. POR. 1 hit.
    PF01855. POR_N. 1 hit.
    PF02775. TPP_enzyme_C. 1 hit.
    [Graphical view ]
    PIRSFi PIRSF000159. NifJ. 1 hit.
    SMARTi SM00890. EKR. 1 hit.
    [Graphical view ]
    SUPFAMi SSF52518. SSF52518. 2 hits.
    SSF52922. SSF52922. 1 hit.
    SSF53323. SSF53323. 1 hit.
    TIGRFAMsi TIGR02176. pyruv_ox_red. 1 hit.
    PROSITEi PS00198. 4FE4S_FER_1. 2 hits.
    PS51379. 4FE4S_FER_2. 2 hits.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    4. "The ldhA gene encoding the fermentative lactate dehydrogenase of Escherichia coli."
      Bunch P.K., Mat-Jan F., Lee N., Clark D.P.
      Microbiology 143:187-195(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-53.
      Strain: K12.
    5. Rudd K.E.
      Unpublished observations (MAR-1996)
      Cited for: IDENTIFICATION.

    Entry informationi

    Entry nameiNIFJ_ECOLI
    AccessioniPrimary (citable) accession number: P52647
    Secondary accession number(s): P77238
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1996
    Last sequence update: November 1, 1997
    Last modified: October 1, 2014
    This is version 132 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3