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P04993 (RECD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 14, 2014. Version 129. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended 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 names
Name:recD
Synonyms:hopE
Ordered Locus Names:b2819, JW2787
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length608 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.6 Ref.7 Ref.8 Ref.9 Ref.10 Ref.11 Ref.12 Ref.13 Ref.14 Ref.15

Catalytic activity

Exonucleolytic cleavage (in the presence of ATP) in either 5'- to 3'- or 3'- to 5'-direction to yield 5'-phosphooligonucleotides. HAMAP-Rule MF_01487

Enzyme regulation

In isolated subunit ATPase and 5'-3' helicase activity are inhibited by non-hydrolyzable ATP analogs and EDTA. Ref.13

Subunit structure

Heterotrimer of RecB, RecC and RecD. All subunits contribute to DNA-binding. Ref.5 Ref.6 Ref.16 Ref.17

Disruption phenotype

Loss of RecBCD enzyme exonuclease activity, no effect on recombination proficiency or resistance to DNA-damaging agents. Ref.5 Ref.12

Sequence similarities

Belongs to the RecD family.

Ontologies

Keywords
   Biological processAntiviral defense
DNA damage
DNA repair
   LigandATP-binding
DNA-binding
Nucleotide-binding
   Molecular functionEndonuclease
Exonuclease
Helicase
Hydrolase
Nuclease
   Technical term3D-structure
Complete proteome
Direct protein sequencing
Reference proteome
Gene Ontology (GO)
   Biological_processATP catabolic process

Inferred from direct assay PubMed 9092551. Source: GOC

DNA catabolic process, exonucleolytic

Inferred from direct assay Ref.6. Source: GOC

DNA recombination

Inferred from direct assay PubMed 2014257. Source: EcoCyc

cellular response to DNA damage stimulus

Inferred from direct assay Ref.6. Source: EcoliWiki

defense response to virus

Inferred from electronic annotation. Source: UniProtKB-KW

double-strand break repair

Inferred from direct assay Ref.15PubMed 2014257. Source: EcoCyc

nucleic acid phosphodiester bond hydrolysis

Inferred from direct assay Ref.6. Source: GOC

   Cellular_componentexodeoxyribonuclease V complex

Inferred from direct assay Ref.6. Source: EcoliWiki

   Molecular_functionATP binding

Inferred from direct assay PubMed 3298248. Source: EcoliWiki

DNA binding

Inferred from electronic annotation. Source: UniProtKB-KW

endonuclease activity

Inferred from direct assay Ref.6. Source: EcoCyc

exodeoxyribonuclease V activity

Inferred from direct assay Ref.6. Source: EcoCyc

helicase activity

Inferred from direct assay PubMed 9092551. Source: EcoCyc

single-stranded DNA-dependent ATPase activity

Inferred from direct assay PubMed 9092551. Source: EcoCyc

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 608608RecBCD enzyme subunit RecD HAMAP-Rule MF_01487
PRO_0000087115

Regions

Nucleotide binding171 – 1788ATP Probable
DNA binding2471 Probable

Experimental info

Mutagenesis1771K → 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. Ref.6 Ref.13 Ref.14
Sequence conflict247 – 2482QP → HR in CAA28253. Ref.1
Sequence conflict3061A → V in CAA28253. Ref.1
Sequence conflict3901F → L in CAA28253. Ref.1

Secondary structure

................................................................................................ 608
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P04993 [UniParc].

Last modified November 1, 1997. Version 2.
Checksum: C37C62E17D41AA82

FASTA60866,902
        10         20         30         40         50         60 
MKLQKQLLEA VEHKQLRPLD VQFALTVAGD EHPAVTLAAA LLSHDAGEGH VCLPLSRLEN 

        70         80         90        100        110        120 
NEASHPLLAT CVSEIGELQN WEECLLASQA VSRGDEPTPM ILCGDRLYLN RMWCNERTVA 

       130        140        150        160        170        180 
RFFNEVNHAI EVDEALLAQT LDKLFPVSDE INWQKVAAAV ALTRRISVIS GGPGTGKTTT 

       190        200        210        220        230        240 
VAKLLAALIQ MADGERCRIR LAAPTGKAAA RLTESLGKAL RQLPLTDEQK KRIPEDASTL 

       250        260        270        280        290        300 
HRLLGAQPGS QRLRHHAGNP LHLDVLVVDE ASMIDLPMMS RLIDALPDHA RVIFLGDRDQ 

       310        320        330        340        350        360 
LASVEAGAVL GDICAYANAG FTAERARQLS RLTGTHVPAG TGTEAASLRD SLCLLQKSYR 

       370        380        390        400        410        420 
FGSDSGIGQL AAAINRGDKT AVKTVFQQDF TDIEKRLLQS GEDYIAMLEE ALAGYGRYLD 

       430        440        450        460        470        480 
LLQARAEPDL IIQAFNEYQL LCALREGPFG VAGLNERIEQ FMQQKRKIHR HPHSRWYEGR 

       490        500        510        520        530        540 
PVMIARNDSA LGLFNGDIGI ALDRGQGTRV WFAMPDGNIK SVQPSRLPEH ETTWAMTVHK 

       550        560        570        580        590        600 
SQGSEFDHAA LILPSQRTPV VTRELVYTAV TRARRRLSLY ADERILSAAI ATRTERRSGL 


AALFSSRE 

« Hide

References

« Hide 'large scale' references
[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]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1462(1997) [PubMed] [Europe PMC] [Abstract]
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]"RecBCD enzyme is a bipolar DNA helicase."
Dillingham M.S., Spies M., Kowalczykowski S.C.
Nature 423:893-897(2003) [PubMed] [Europe PMC] [Abstract]
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]"An end-joining repair mechanism in Escherichia coli."
Chayot R., Montagne B., Mazel D., Ricchetti M.
Proc. Natl. Acad. Sci. U.S.A. 107:2141-2146(2010) [PubMed] [Europe PMC] [Abstract]
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.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRNCECXF. D65064.
RefSeqNP_417296.1. NC_000913.3.
YP_491024.1. NC_007779.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1W36X-ray3.10D/G1-608[»]
3K70X-ray3.59D/G1-608[»]
ProteinModelPortalP04993.
SMRP04993. Positions 1-466, 523-606.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

DIPDIP-10651N.
IntActP04993. 13 interactions.
MINTMINT-1224412.
STRING511145.b2819.

Chemistry

BindingDBP04993.
ChEMBLCHEMBL2095232.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC75858; AAC75858; b2819.
BAE76888; BAE76888; BAE76888.
GeneID12931690.
947287.
KEGGecj:Y75_p2753.
eco:b2819.
PATRIC32121056. VBIEscCol129921_2917.

Organism-specific databases

EchoBASEEB0819.
EcoGeneEG10826. recD.

Phylogenomic databases

eggNOGCOG0507.
HOGENOMHOG000258341.
KOK03581.
OMARMWRNEL.
OrthoDBEOG60GRSZ.
PhylomeDBP04993.

Enzyme and pathway databases

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

Gene expression databases

GenevestigatorP04993.

Family and domain databases

Gene3D3.40.50.300. 3 hits.
HAMAPMF_01487. RecD.
InterProIPR003593. AAA+_ATPase.
IPR006344. ExoDNase_V_RecD_asu.
IPR027417. P-loop_NTPase.
IPR027785. UvrD_like_helicase_C.
[Graphical view]
PfamPF13538. UvrD_C_2. 1 hit.
[Graphical view]
SMARTSM00382. AAA. 1 hit.
[Graphical view]
SUPFAMSSF52540. SSF52540. 3 hits.
TIGRFAMsTIGR01447. recD. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP04993.
PROP04993.

Entry information

Entry nameRECD_ECOLI
AccessionPrimary (citable) accession number: P04993
Secondary accession number(s): Q2MA18, Q59378
Entry history
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 statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene