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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 (>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

Enzyme 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

  • 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
  • DNA recombination Source: EcoliWiki
  • double-strand break repair Source: EcoCyc
  • double-strand break repair via homologous recombination Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Exonuclease, Helicase, Hydrolase, Nuclease

Keywords - Biological processi

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 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)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.
DIPiDIP-10651N.
IntActiP04993. 13 interactors.
MINTiMINT-1224412.
STRINGi511145.b2819.

Chemistry databases

BindingDBiP04993.

Structurei

Secondary structure

1608
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi4 – 12Combined sources9
Helixi18 – 27Combined sources10
Beta strandi28 – 31Combined sources4
Helixi33 – 47Combined sources15
Beta strandi51 – 54Combined sources4
Turni55 – 60Combined sources6
Helixi61 – 64Combined sources4
Beta strandi65 – 67Combined sources3
Helixi81 – 87Combined sources7
Beta strandi91 – 96Combined sources6
Beta strandi99 – 102Combined sources4
Beta strandi104 – 109Combined sources6
Helixi110 – 123Combined sources14
Helixi134 – 142Combined sources9
Helixi153 – 162Combined sources10
Beta strandi164 – 170Combined sources7
Helixi177 – 190Combined sources14
Beta strandi199 – 205Combined sources7
Helixi206 – 216Combined sources11
Helixi218 – 222Combined sources5
Turni239 – 241Combined sources3
Beta strandi264 – 268Combined sources5
Helixi271 – 273Combined sources3
Helixi276 – 284Combined sources9
Beta strandi291 – 296Combined sources6
Helixi301 – 303Combined sources3
Helixi310 – 313Combined sources4
Helixi314 – 317Combined sources4
Helixi323 – 332Combined sources10
Beta strandi333 – 335Combined sources3
Helixi346 – 349Combined sources4
Beta strandi352 – 354Combined sources3
Helixi367 – 374Combined sources8
Helixi378 – 382Combined sources5
Turni383 – 385Combined sources3
Helixi387 – 389Combined sources3
Beta strandi392 – 394Combined sources3
Turni401 – 403Combined sources3
Helixi404 – 414Combined sources11
Helixi416 – 423Combined sources8
Helixi432 – 435Combined sources4
Beta strandi438 – 443Combined sources6
Beta strandi445 – 450Combined sources6
Helixi451 – 459Combined sources9
Helixi460 – 462Combined sources3
Beta strandi534 – 537Combined sources4
Turni538 – 543Combined sources6
Beta strandi546 – 552Combined sources7
Beta strandi559 – 561Combined sources3
Helixi563 – 570Combined sources8
Beta strandi573 – 575Combined sources3
Beta strandi577 – 580Combined sources4
Helixi585 – 591Combined sources7
Helixi600 – 603Combined sources4

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[»]
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.
OMAiNRERYLP.
PhylomeDBiP04993.

Family and domain databases

Gene3Di3.40.50.300. 3 hits.
HAMAPiMF_01487. RecD. 1 hit.
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)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.
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_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[»]
ProteinModelPortaliP04993.
SMRiP04993.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260684. 132 interactors.
DIPiDIP-10651N.
IntActiP04993. 13 interactors.
MINTiMINT-1224412.
STRINGi511145.b2819.

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.
PATRICi32121056. VBIEscCol129921_2917.

Organism-specific databases

EchoBASEiEB0819.
EcoGeneiEG10826. recD.

Phylogenomic databases

eggNOGiENOG4107QYX. Bacteria.
COG0507. LUCA.
HOGENOMiHOG000258341.
InParanoidiP04993.
KOiK03581.
OMAiNRERYLP.
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. 1 hit.
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...

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: November 30, 2016
This is version 149 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

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 one 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.