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P04993

- RECD_ECOLI

UniProt

P04993 - RECD_ECOLI

Protein

RecBCD enzyme subunit RecD

Gene

recD

Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 130 (01 Oct 2014)
      Sequence version 2 (01 Nov 1997)
      Previous versions | rss
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    Functioni

    A helicase/nuclease that prepares dsDNA breaks (DSB) for recombinational DNA repair. Binds to DSBs and unwinds DNA via a rapid and highly processive ATP-dependent bidirectional helicase (1350 bp/s). Degrades the ssDNA until it encounters a chi (crossover hotspot instigator, 5'-GCTGGTGG-3') sequence from the 3' direction. Cuts DNA near or within the chi site, attentuating 3'- but not 5'-exonuclease activity. The altered holoenzyme produces a long 3'-ssDNA overhang which facilitates RecA-binding to the ssDNA for homologous DNA recombination and repair. Holoenzyme degrades foreign DNA, contributing to antiviral protection. It may also be involved in alternative end-joining, a modified version of non-homologous end-joining of DSBs. This subunit has ssDNA-dependent ATPase and 5'-3' helicase activity. When added to pre-assembled RecBC greatly stimulates nuclease activity and augments holoenzyme processivity. Negatively regulates the RecA-loading ability of RecBCD.9 Publications

    Catalytic activityi

    Exonucleolytic cleavage (in the presence of ATP) in either 5'- to 3'- or 3'- to 5'-direction to yield 5'-phosphooligonucleotides.UniRule annotation

    Enzyme regulationi

    In isolated subunit ATPase and 5'-3' helicase activity are inhibited by non-hydrolyzable ATP analogs and EDTA.1 Publication

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi171 – 1788ATPCurated
    DNA bindingi247 – 2471Curated

    GO - Molecular functioni

    1. ATP binding Source: EcoliWiki
    2. DNA binding Source: UniProtKB-KW
    3. endonuclease activity Source: EcoCyc
    4. exodeoxyribonuclease V activity Source: EcoCyc
    5. helicase activity Source: EcoCyc
    6. single-stranded DNA-dependent ATPase activity Source: EcoCyc

    GO - Biological processi

    1. ATP catabolic process Source: GOC
    2. cellular response to DNA damage stimulus Source: EcoliWiki
    3. defense response to virus Source: UniProtKB-KW
    4. DNA catabolic process, exonucleolytic Source: GOC
    5. DNA recombination Source: EcoCyc
    6. double-strand break repair Source: EcoCyc
    7. nucleic acid phosphodiester bond hydrolysis Source: GOC

    Keywords - Molecular functioni

    Endonuclease, Exonuclease, Helicase, Hydrolase, Nuclease

    Keywords - Biological processi

    Antiviral defense, DNA damage, DNA repair

    Keywords - Ligandi

    ATP-binding, DNA-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG10826-MONOMER.
    ECOL316407:JW2787-MONOMER.
    MetaCyc:EG10826-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    RecBCD enzyme subunit RecDUniRule annotation (EC:3.1.11.5UniRule annotation)
    Alternative name(s):
    Exodeoxyribonuclease V 67 kDa polypeptide
    Exodeoxyribonuclease V alpha chain
    Exonuclease V subunit RecDUniRule annotation
    Short name:
    ExoV subunit RecDUniRule annotation
    Helicase/nuclease RecBCD subunit RecDUniRule annotation
    Gene namesi
    Name:recDUniRule annotation
    Synonyms:hopE
    Ordered Locus Names:b2819, JW2787
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318: Chromosome, UP000000625: Chromosome

    Organism-specific databases

    EcoGeneiEG10826. recD.

    Subcellular locationi

    GO - Cellular componenti

    1. exodeoxyribonuclease V complex Source: EcoliWiki

    Pathology & Biotechi

    Disruption phenotypei

    Loss of RecBCD enzyme exonuclease activity, no effect on recombination proficiency or resistance to DNA-damaging agents.2 Publications

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi177 – 1771K → Q: Loss of ATP-dependent exonuclease activity in holoenzyme. Subunit loses ATPase and 5'-3' helicase activity, holoenzyme has 2-fold less helicase activity, 5-fold less processivity. 3 Publications

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 608608RecBCD enzyme subunit RecDPRO_0000087115Add
    BLAST

    Expressioni

    Gene expression databases

    GenevestigatoriP04993.

    Interactioni

    Subunit structurei

    Heterotrimer of RecB, RecC and RecD. All subunits contribute to DNA-binding.4 PublicationsUniRule annotation

    Protein-protein interaction databases

    DIPiDIP-10651N.
    IntActiP04993. 13 interactions.
    MINTiMINT-1224412.
    STRINGi511145.b2819.

    Structurei

    Secondary structure

    1
    608
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi4 – 129
    Helixi18 – 2710
    Beta strandi28 – 314
    Helixi33 – 4715
    Beta strandi51 – 544
    Turni55 – 606
    Helixi61 – 644
    Beta strandi65 – 673
    Helixi81 – 877
    Beta strandi91 – 966
    Beta strandi99 – 1024
    Beta strandi104 – 1096
    Helixi110 – 12314
    Helixi134 – 1429
    Helixi153 – 16210
    Beta strandi164 – 1707
    Helixi177 – 19014
    Beta strandi199 – 2057
    Helixi206 – 21611
    Helixi218 – 2225
    Turni239 – 2413
    Beta strandi264 – 2685
    Helixi271 – 2733
    Helixi276 – 2849
    Beta strandi291 – 2966
    Helixi301 – 3033
    Helixi310 – 3134
    Helixi314 – 3174
    Helixi323 – 33210
    Beta strandi333 – 3353
    Helixi346 – 3494
    Beta strandi352 – 3543
    Helixi367 – 3748
    Helixi378 – 3825
    Turni383 – 3853
    Helixi387 – 3893
    Beta strandi392 – 3943
    Turni401 – 4033
    Helixi404 – 41411
    Helixi416 – 4238
    Helixi432 – 4354
    Beta strandi438 – 4436
    Beta strandi445 – 4506
    Helixi451 – 4599
    Helixi460 – 4623
    Beta strandi534 – 5374
    Turni538 – 5436
    Beta strandi546 – 5527
    Beta strandi559 – 5613
    Helixi563 – 5708
    Beta strandi573 – 5753
    Beta strandi577 – 5804
    Helixi585 – 5917
    Helixi600 – 6034

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1W36X-ray3.10D/G1-608[»]
    3K70X-ray3.59D/G1-608[»]
    ProteinModelPortaliP04993.
    SMRiP04993. Positions 1-466, 523-606.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP04993.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the RecD family.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0507.
    HOGENOMiHOG000258341.
    KOiK03581.
    OMAiRMWRNEL.
    OrthoDBiEOG60GRSZ.
    PhylomeDBiP04993.

    Family and domain databases

    Gene3Di3.40.50.300. 3 hits.
    HAMAPiMF_01487. RecD.
    InterProiIPR003593. AAA+_ATPase.
    IPR006344. ExoDNase_V_RecD_asu.
    IPR027417. P-loop_NTPase.
    IPR027785. UvrD_like_helicase_C.
    [Graphical view]
    PfamiPF13538. UvrD_C_2. 1 hit.
    [Graphical view]
    SMARTiSM00382. AAA. 1 hit.
    [Graphical view]
    SUPFAMiSSF52540. SSF52540. 3 hits.
    TIGRFAMsiTIGR01447. recD. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P04993-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKLQKQLLEA VEHKQLRPLD VQFALTVAGD EHPAVTLAAA LLSHDAGEGH    50
    VCLPLSRLEN NEASHPLLAT CVSEIGELQN WEECLLASQA VSRGDEPTPM 100
    ILCGDRLYLN RMWCNERTVA RFFNEVNHAI EVDEALLAQT LDKLFPVSDE 150
    INWQKVAAAV ALTRRISVIS GGPGTGKTTT VAKLLAALIQ MADGERCRIR 200
    LAAPTGKAAA RLTESLGKAL RQLPLTDEQK KRIPEDASTL HRLLGAQPGS 250
    QRLRHHAGNP LHLDVLVVDE ASMIDLPMMS RLIDALPDHA RVIFLGDRDQ 300
    LASVEAGAVL GDICAYANAG FTAERARQLS RLTGTHVPAG TGTEAASLRD 350
    SLCLLQKSYR FGSDSGIGQL AAAINRGDKT AVKTVFQQDF TDIEKRLLQS 400
    GEDYIAMLEE ALAGYGRYLD LLQARAEPDL IIQAFNEYQL LCALREGPFG 450
    VAGLNERIEQ FMQQKRKIHR HPHSRWYEGR PVMIARNDSA LGLFNGDIGI 500
    ALDRGQGTRV WFAMPDGNIK SVQPSRLPEH ETTWAMTVHK SQGSEFDHAA 550
    LILPSQRTPV VTRELVYTAV TRARRRLSLY ADERILSAAI ATRTERRSGL 600
    AALFSSRE 608
    Length:608
    Mass (Da):66,902
    Last modified:November 1, 1997 - v2
    Checksum:iC37C62E17D41AA82
    GO

    Experimental Info

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti247 – 2482QP → HR in CAA28253. (PubMed:3537961)Curated
    Sequence conflicti306 – 3061A → V in CAA28253. (PubMed:3537961)Curated
    Sequence conflicti390 – 3901F → L in CAA28253. (PubMed:3537961)Curated

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X04582 Genomic DNA. Translation: CAA28253.1.
    U29581 Genomic DNA. Translation: AAB40466.1.
    U00096 Genomic DNA. Translation: AAC75858.1.
    AP009048 Genomic DNA. Translation: BAE76888.1.
    X04581 Genomic DNA. Translation: CAA28251.1.
    PIRiD65064. NCECXF.
    RefSeqiNP_417296.1. NC_000913.3.
    YP_491024.1. NC_007779.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75858; AAC75858; b2819.
    BAE76888; BAE76888; BAE76888.
    GeneIDi12931690.
    947287.
    KEGGiecj:Y75_p2753.
    eco:b2819.
    PATRICi32121056. VBIEscCol129921_2917.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    X04582 Genomic DNA. Translation: CAA28253.1 .
    U29581 Genomic DNA. Translation: AAB40466.1 .
    U00096 Genomic DNA. Translation: AAC75858.1 .
    AP009048 Genomic DNA. Translation: BAE76888.1 .
    X04581 Genomic DNA. Translation: CAA28251.1 .
    PIRi D65064. NCECXF.
    RefSeqi NP_417296.1. NC_000913.3.
    YP_491024.1. NC_007779.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1W36 X-ray 3.10 D/G 1-608 [» ]
    3K70 X-ray 3.59 D/G 1-608 [» ]
    ProteinModelPortali P04993.
    SMRi P04993. Positions 1-466, 523-606.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-10651N.
    IntActi P04993. 13 interactions.
    MINTi MINT-1224412.
    STRINGi 511145.b2819.

    Chemistry

    BindingDBi P04993.
    ChEMBLi CHEMBL2095232.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAC75858 ; AAC75858 ; b2819 .
    BAE76888 ; BAE76888 ; BAE76888 .
    GeneIDi 12931690.
    947287.
    KEGGi ecj:Y75_p2753.
    eco:b2819.
    PATRICi 32121056. VBIEscCol129921_2917.

    Organism-specific databases

    EchoBASEi EB0819.
    EcoGenei EG10826. recD.

    Phylogenomic databases

    eggNOGi COG0507.
    HOGENOMi HOG000258341.
    KOi K03581.
    OMAi RMWRNEL.
    OrthoDBi EOG60GRSZ.
    PhylomeDBi P04993.

    Enzyme and pathway databases

    BioCyci EcoCyc:EG10826-MONOMER.
    ECOL316407:JW2787-MONOMER.
    MetaCyc:EG10826-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei P04993.
    PROi P04993.

    Gene expression databases

    Genevestigatori P04993.

    Family and domain databases

    Gene3Di 3.40.50.300. 3 hits.
    HAMAPi MF_01487. RecD.
    InterProi IPR003593. AAA+_ATPase.
    IPR006344. ExoDNase_V_RecD_asu.
    IPR027417. P-loop_NTPase.
    IPR027785. UvrD_like_helicase_C.
    [Graphical view ]
    Pfami PF13538. UvrD_C_2. 1 hit.
    [Graphical view ]
    SMARTi SM00382. AAA. 1 hit.
    [Graphical view ]
    SUPFAMi SSF52540. SSF52540. 3 hits.
    TIGRFAMsi TIGR01447. recD. 1 hit.
    ProtoNeti Search...

    Publicationsi

    1. "Complete nucleotide sequence of recD, the structural gene for the alpha subunit of Exonuclease V of Escherichia coli."
      Finch P.W., Storey A., Brown K., Hickson I.D., Emmerson P.T.
      Nucleic Acids Res. 14:8583-8594(1986) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    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. "Complete nucleotide sequence of the Escherichia coli recB gene."
      Finch P.W., Storey A., Chapman K.E., Brown K., Hickson I.D., Emmerson P.T.
      Nucleic Acids Res. 14:8573-8582(1986) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-31.
    5. "recD: the gene for an essential third subunit of exonuclease V."
      Amundsen S.K., Taylor A.F., Chaudhury A.M., Smith G.R.
      Proc. Natl. Acad. Sci. U.S.A. 83:5558-5562(1986) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION, OPERON, SUBUNIT, DISRUPTION PHENOTYPE.
    6. "Reconstitution of the activities of the RecBCD holoenzyme of Escherichia coli from the purified subunits."
      Masterson C., Boehmer P.E., McDonald F., Chaudhuri S., Hickson I.D., Emmerson P.T.
      J. Biol. Chem. 267:13564-13572(1992) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-10, FUNCTION AS AN EXONUCLEASE; ENDONUCLEASE; HELICASE AND ATPASE, SUBUNIT, MUTAGENESIS OF LYS-177.
    7. "Role of the Escherichia coli recombination hotspot, chi, in RecABCD-dependent homologous pairing."
      Dixon D.A., Kowalczykowski S.C.
      J. Biol. Chem. 270:16360-16370(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN HOMOLOGOUS RECOMBINATION.
    8. "The translocating RecBCD enzyme stimulates recombination by directing RecA protein onto ssDNA in a chi-regulated manner."
      Anderson D.G., Kowalczykowski S.C.
      Cell 90:77-86(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN RECA-LOADING.
    9. "The recombination hotspot Chi is recognized by the translocating RecBCD enzyme as the single strand of DNA containing the sequence 5'-GCTGGTGG-3'."
      Bianco P.R., Kowalczykowski S.C.
      Proc. Natl. Acad. Sci. U.S.A. 94:6706-6711(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN RECOGNITION OF CHI.
    10. "Identification of the nuclease active site in the multifunctional RecBCD enzyme by creation of a chimeric enzyme."
      Yu M., Souaya J., Julin D.A.
      J. Mol. Biol. 283:797-808(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    11. "The 30-kDa C-terminal domain of the RecB protein is critical for the nuclease activity, but not the helicase activity, of the RecBCD enzyme from Escherichia coli."
      Yu M., Souaya J., Julin D.A.
      Proc. Natl. Acad. Sci. U.S.A. 95:981-986(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    12. "The RecD subunit of the Escherichia coli RecBCD enzyme inhibits RecA loading, homologous recombination, and DNA repair."
      Amundsen S.K., Taylor A.F., Smith G.R.
      Proc. Natl. Acad. Sci. U.S.A. 97:7399-7404(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION IN RECA-LOADING, DISRUPTION PHENOTYPE.
    13. Cited for: FUNCTION AS AN ATPASE, FUNCTION AS A 5'-3' HELICASE, ENZYME REGULATION, MUTAGENESIS OF LYS-177.
    14. "Bipolar DNA translocation contributes to highly processive DNA unwinding by RecBCD enzyme."
      Dillingham M.S., Webb M.R., Kowalczykowski S.C.
      J. Biol. Chem. 280:37069-37077(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, RATE, DNA-BINDING, MUTAGENESIS OF LYS-177.
    15. Cited for: POSSIBLE FUNCTION IN ALTERNATIVE END-JOINING.
      Strain: K12 / TG1.
    16. "Crystal structure of RecBCD enzyme reveals a machine for processing DNA breaks."
      Singleton M.R., Dillingham M.S., Gaudier M., Kowalczykowski S.C., Wigley D.B.
      Nature 432:187-193(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.1 ANGSTROMS) IN COMPLEX WITH DNA, SUBUNIT.
    17. "DNA binding to RecD: role of the 1B domain in SF1B helicase activity."
      Saikrishnan K., Griffiths S.P., Cook N., Court R., Wigley D.B.
      EMBO J. 27:2222-2229(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.59 ANGSTROMS) IN COMPLEX WITH DNA, SUBUNIT.
    18. "RecBCD enzyme and the repair of double-stranded DNA breaks."
      Dillingham M.S., Kowalczykowski S.C.
      Microbiol. Mol. Biol. Rev. 72:642-671(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: REVIEW.

    Entry informationi

    Entry nameiRECD_ECOLI
    AccessioniPrimary (citable) accession number: P04993
    Secondary accession number(s): Q2MA18, Q59378
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: August 13, 1987
    Last sequence update: November 1, 1997
    Last modified: October 1, 2014
    This is version 130 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

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

    Documents

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

    External Data

    Dasty 3