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P04993

- RECD_ECOLI

UniProt

P04993 - RECD_ECOLI

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Protein

RecBCD enzyme subunit RecD

Gene
recD, hopE, b2819, JW2787
Organism
Escherichia coli (strain K12)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

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.10 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 – 1788ATP Inferred
DNA bindingi247 – 2471 Inferred

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
Complete GO annotation...

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 RecD (EC:3.1.11.5)
Alternative name(s):
Exodeoxyribonuclease V 67 kDa polypeptide
Exodeoxyribonuclease V alpha chain
Exonuclease V subunit RecD
Short name:
ExoV subunit RecD
Helicase/nuclease RecBCD subunit RecD
Gene namesi
Name:recD
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
Complete GO annotation...

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 RecDUniRule annotationPRO_0000087115Add
BLAST

Expressioni

Gene expression databases

GenevestigatoriP04993.

Interactioni

Subunit structurei

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

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.

Miscellaneous databases

EvolutionaryTraceiP04993.

Family & Domainsi

Sequence similaritiesi

Belongs to the RecD family.

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

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti247 – 2482QP → HR in CAA28253. 1 Publication
Sequence conflicti306 – 3061A → V in CAA28253. 1 Publication
Sequence conflicti390 – 3901F → L in CAA28253. 1 Publication

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

« Hide 'large scale' publications
  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: May 14, 2014
This is version 129 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

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