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Protein

RecBCD enzyme subunit RecD

Gene

recD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: 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.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

  • ATP binding Source: EcoliWiki
  • ATP-dependent DNA helicase activity Source: UniProtKB-HAMAP
  • DNA binding Source: UniProtKB-HAMAP
  • endonuclease activity Source: EcoCyc
  • exodeoxyribonuclease V activity Source: EcoCyc
  • helicase activity Source: EcoCyc
  • single-stranded DNA-dependent ATPase activity Source: EcoCyc

GO - Biological processi

  • cellular response to DNA damage stimulus Source: EcoliWiki
  • defense response to virus Source: UniProtKB-KW
  • DNA recombination Source: EcoliWiki
  • double-strand break repair Source: EcoCyc
  • double-strand break repair via homologous recombination Source: UniProtKB-HAMAP
  • 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.
BRENDAi3.1.11.5. 2026.

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 Componenti: Chromosome UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10826. recD.

Subcellular locationi

GO - Cellular componenti

  • 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 RecDPRO_0000087115Add
BLAST

Interactioni

Subunit structurei

Heterotrimer of RecB, RecC and RecD. All subunits contribute to DNA-binding.UniRule annotation4 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 – 129Combined sources
Helixi18 – 2710Combined sources
Beta strandi28 – 314Combined sources
Helixi33 – 4715Combined sources
Beta strandi51 – 544Combined sources
Turni55 – 606Combined sources
Helixi61 – 644Combined sources
Beta strandi65 – 673Combined sources
Helixi81 – 877Combined sources
Beta strandi91 – 966Combined sources
Beta strandi99 – 1024Combined sources
Beta strandi104 – 1096Combined sources
Helixi110 – 12314Combined sources
Helixi134 – 1429Combined sources
Helixi153 – 16210Combined sources
Beta strandi164 – 1707Combined sources
Helixi177 – 19014Combined sources
Beta strandi199 – 2057Combined sources
Helixi206 – 21611Combined sources
Helixi218 – 2225Combined sources
Turni239 – 2413Combined sources
Beta strandi264 – 2685Combined sources
Helixi271 – 2733Combined sources
Helixi276 – 2849Combined sources
Beta strandi291 – 2966Combined sources
Helixi301 – 3033Combined sources
Helixi310 – 3134Combined sources
Helixi314 – 3174Combined sources
Helixi323 – 33210Combined sources
Beta strandi333 – 3353Combined sources
Helixi346 – 3494Combined sources
Beta strandi352 – 3543Combined sources
Helixi367 – 3748Combined sources
Helixi378 – 3825Combined sources
Turni383 – 3853Combined sources
Helixi387 – 3893Combined sources
Beta strandi392 – 3943Combined sources
Turni401 – 4033Combined sources
Helixi404 – 41411Combined sources
Helixi416 – 4238Combined sources
Helixi432 – 4354Combined sources
Beta strandi438 – 4436Combined sources
Beta strandi445 – 4506Combined sources
Helixi451 – 4599Combined sources
Helixi460 – 4623Combined sources
Beta strandi534 – 5374Combined sources
Turni538 – 5436Combined sources
Beta strandi546 – 5527Combined sources
Beta strandi559 – 5613Combined sources
Helixi563 – 5708Combined sources
Beta strandi573 – 5753Combined sources
Beta strandi577 – 5804Combined sources
Helixi585 – 5917Combined sources
Helixi600 – 6034Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
InParanoidiP04993.
KOiK03581.
OMAiNRERYLP.
OrthoDBiEOG60GRSZ.
PhylomeDBiP04993.

Family and domain databases

Gene3Di3.40.50.300. 3 hits.
HAMAPiMF_01487. RecD.
InterProiIPR003593. AAA+_ATPase.
IPR027417. P-loop_NTPase.
IPR006344. RecD.
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

        10         20         30         40         50
MKLQKQLLEA VEHKQLRPLD VQFALTVAGD EHPAVTLAAA LLSHDAGEGH
60 70 80 90 100
VCLPLSRLEN NEASHPLLAT CVSEIGELQN WEECLLASQA VSRGDEPTPM
110 120 130 140 150
ILCGDRLYLN RMWCNERTVA RFFNEVNHAI EVDEALLAQT LDKLFPVSDE
160 170 180 190 200
INWQKVAAAV ALTRRISVIS GGPGTGKTTT VAKLLAALIQ MADGERCRIR
210 220 230 240 250
LAAPTGKAAA RLTESLGKAL RQLPLTDEQK KRIPEDASTL HRLLGAQPGS
260 270 280 290 300
QRLRHHAGNP LHLDVLVVDE ASMIDLPMMS RLIDALPDHA RVIFLGDRDQ
310 320 330 340 350
LASVEAGAVL GDICAYANAG FTAERARQLS RLTGTHVPAG TGTEAASLRD
360 370 380 390 400
SLCLLQKSYR FGSDSGIGQL AAAINRGDKT AVKTVFQQDF TDIEKRLLQS
410 420 430 440 450
GEDYIAMLEE ALAGYGRYLD LLQARAEPDL IIQAFNEYQL LCALREGPFG
460 470 480 490 500
VAGLNERIEQ FMQQKRKIHR HPHSRWYEGR PVMIARNDSA LGLFNGDIGI
510 520 530 540 550
ALDRGQGTRV WFAMPDGNIK SVQPSRLPEH ETTWAMTVHK SQGSEFDHAA
560 570 580 590 600
LILPSQRTPV VTRELVYTAV TRARRRLSLY ADERILSAAI ATRTERRSGL

AALFSSRE
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:
EMBLi
GenBanki
DDBJi
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.
WP_000775955.1. NZ_CP010445.1.

Genome annotation databases

EnsemblBacteriaiAAC75858; AAC75858; b2819.
BAE76888; BAE76888; BAE76888.
GeneIDi947287.
KEGGieco:b2819.
PATRICi32121056. VBIEscCol129921_2917.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
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.
WP_000775955.1. NZ_CP010445.1.

3D structure databases

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

Protein-protein interaction databases

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

Chemistry

BindingDBiP04993.
ChEMBLiCHEMBL2095232.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75858; AAC75858; b2819.
BAE76888; BAE76888; BAE76888.
GeneIDi947287.
KEGGieco:b2819.
PATRICi32121056. VBIEscCol129921_2917.

Organism-specific databases

EchoBASEiEB0819.
EcoGeneiEG10826. recD.

Phylogenomic databases

eggNOGiCOG0507.
HOGENOMiHOG000258341.
InParanoidiP04993.
KOiK03581.
OMAiNRERYLP.
OrthoDBiEOG60GRSZ.
PhylomeDBiP04993.

Enzyme and pathway databases

BioCyciEcoCyc:EG10826-MONOMER.
ECOL316407:JW2787-MONOMER.
MetaCyc:EG10826-MONOMER.
BRENDAi3.1.11.5. 2026.

Miscellaneous databases

EvolutionaryTraceiP04993.
PROiP04993.

Family and domain databases

Gene3Di3.40.50.300. 3 hits.
HAMAPiMF_01487. RecD.
InterProiIPR003593. AAA+_ATPase.
IPR027417. P-loop_NTPase.
IPR006344. RecD.
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.
ProtoNetiSearch...

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: July 22, 2015
This is version 139 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

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 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.