Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

RecBCD enzyme subunit RecD

Gene

recD

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -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 (>1 kb/second) and highly processive (>30 kb) ATP-dependent bidirectional helicase. Unwinds dsDNA until it encounters a Chi (crossover hotspot instigator, 5'-GCTGGTGG-3') sequence from the 3' direction. Cuts ssDNA a few nucleotides 3' to Chi site, by nicking one strand or switching the strand degraded (depending on the reaction conditions). The properties and activities of the enzyme are changed at Chi. The Chi-altered holoenzyme produces a long 3'-ssDNA overhang which facilitates RecA-binding to the ssDNA for homologous DNA recombination and repair. In the holoenzyme this subunit contributes ssDNA-dependent ATPase and fast 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.14 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

Activity regulationi

In isolated subunit ATPase and 5'-3' helicase activity are inhibited by non-hydrolyzable ATP analogs and EDTA (PubMed:12815438). After reacting with DNA bearing a Chi site the holoenzyme is disassembled and loses exonuclease activity, DNA unwinding and Chi-directed DNA cleavage; RecB remains complexed with ssDNA, which may prevent holoenzyme reassembly (PubMed:10197988). High levels of Mg2+ (13 mM MgCl2+) or incubation with DNase allow holoenyzme reassembly, suggesting it is DNA bound to RecB that prevents reassembly (PubMed:10197988).3 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi171 – 178ATPCurated8
DNA bindingi247Curated1

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, Exonuclease, Helicase, Hydrolase, Nuclease
Biological processDNA damage, DNA repair
LigandATP-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG10826-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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10826 recD

Subcellular locationi

GO - Cellular componenti

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)DescriptionActionsGraphical viewLength
Mutagenesisi177K → Q: Loss of ATP-dependent exonuclease activity in holoenzyme. Subunit loses ATPase and has ~5% 5'-3' helicase activity, holoenzyme has 2-4 fold less helicase activity, 5-fold less processivity. 6 Publications1

Chemistry databases

ChEMBLiCHEMBL2095232

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000871151 – 608RecBCD enzyme subunit RecDAdd BLAST608

Proteomic databases

PaxDbiP04993
PRIDEiP04993

Interactioni

Subunit structurei

Heterotrimer of RecB, RecC and RecD. All subunits contribute to DNA-binding.UniRule annotation4 Publications

Protein-protein interaction databases

BioGridi4260684, 132 interactors
ComplexPortaliCPX-2197 Exodeoxyribonuclease V complex
DIPiDIP-10651N
IntActiP04993, 13 interactors
MINTiP04993
STRINGi316385.ECDH10B_2989

Chemistry databases

BindingDBiP04993

Structurei

Secondary structure

1608
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP04993
SMRiP04993
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP04993

Family & Domainsi

Domaini

The holoenzyme may undergo conformational shifts upon DNA binding: the nuclease domain of RecB may swing away from the DNA exit tunnel in RecC. When Chi DNA binds to the RecC tunnel the nuclease domain may then swing back to its original position (that seen in crystal structures), allowing it to nick the DNA 3' of the Chi site and then rotate to load RecA. At high Mg2+ the nuclease domain may swing back more frequently, explaining differences seen in assays performed at high Mg2+.1 Publication

Sequence similaritiesi

Belongs to the RecD family.UniRule annotation

Phylogenomic databases

eggNOGiENOG4107QYX Bacteria
COG0507 LUCA
HOGENOMiHOG000258341
InParanoidiP04993
KOiK03581
PhylomeDBiP04993

Family and domain databases

HAMAPiMF_01487 RecD, 1 hit
InterProiView protein in InterPro
IPR003593 AAA+_ATPase
IPR027417 P-loop_NTPase
IPR006344 RecD
IPR027785 UvrD-like_helicase_C
PfamiView protein in Pfam
PF13538 UvrD_C_2, 1 hit
SMARTiView protein in SMART
SM00382 AAA, 1 hit
SUPFAMiSSF52540 SSF52540, 2 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)DescriptionActionsGraphical viewLength
Sequence conflicti247 – 248QP → HR in CAA28253 (PubMed:3537961).Curated2
Sequence conflicti306A → V in CAA28253 (PubMed:3537961).Curated1
Sequence conflicti390F → L in CAA28253 (PubMed:3537961).Curated1

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_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC75858; AAC75858; b2819
BAE76888; BAE76888; BAE76888
GeneIDi947287
KEGGiecj:JW2787
eco:b2819
PATRICifig|1411691.4.peg.3917

Similar proteinsi

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_LN832404.1

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1W36X-ray3.10D/G1-608[»]
3K70X-ray3.59D/G1-608[»]
5LD2electron microscopy3.83D2-608[»]
5MBVelectron microscopy3.80D2-608[»]
ProteinModelPortaliP04993
SMRiP04993
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260684, 132 interactors
ComplexPortaliCPX-2197 Exodeoxyribonuclease V complex
DIPiDIP-10651N
IntActiP04993, 13 interactors
MINTiP04993
STRINGi316385.ECDH10B_2989

Chemistry databases

BindingDBiP04993
ChEMBLiCHEMBL2095232

Proteomic databases

PaxDbiP04993
PRIDEiP04993

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75858; AAC75858; b2819
BAE76888; BAE76888; BAE76888
GeneIDi947287
KEGGiecj:JW2787
eco:b2819
PATRICifig|1411691.4.peg.3917

Organism-specific databases

EchoBASEiEB0819
EcoGeneiEG10826 recD

Phylogenomic databases

eggNOGiENOG4107QYX Bacteria
COG0507 LUCA
HOGENOMiHOG000258341
InParanoidiP04993
KOiK03581
PhylomeDBiP04993

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiP04993
PROiPR:P04993

Family and domain databases

HAMAPiMF_01487 RecD, 1 hit
InterProiView protein in InterPro
IPR003593 AAA+_ATPase
IPR027417 P-loop_NTPase
IPR006344 RecD
IPR027785 UvrD-like_helicase_C
PfamiView protein in Pfam
PF13538 UvrD_C_2, 1 hit
SMARTiView protein in SMART
SM00382 AAA, 1 hit
SUPFAMiSSF52540 SSF52540, 2 hits
TIGRFAMsiTIGR01447 recD, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiRECD_ECOLI
AccessioniPrimary (citable) accession number: P04993
Secondary accession number(s): Q2MA18, Q59378
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: November 1, 1997
Last modified: November 7, 2018
This is version 161 of the entry and version 2 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health

We'd like to inform you that we have updated our Privacy Notice to comply with Europe’s new General Data Protection Regulation (GDPR) that applies since 25 May 2018.

Do not show this banner again