UniProtKB - P04993 (RECD_ECOLI)
Protein
RecBCD enzyme subunit RecD
Gene
recD
Organism
Escherichia coli (strain K12)
Status
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 EC:3.1.11.5
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 key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Nucleotide bindingi | 171 – 178 | ATPCurated | 8 | |
DNA bindingi | 247 | Curated | 1 |
GO - Molecular functioni
- ATP binding Source: EcoliWiki
- DNA binding Source: UniProtKB-UniRule
- exodeoxyribonuclease V activity Source: EcoCyc
- helicase activity Source: EcoCyc
- single-stranded DNA helicase activity Source: EcoCyc
GO - Biological processi
- cellular response to DNA damage stimulus Source: EcoliWiki
- DNA recombination Source: EcoliWiki
- double-strand break repair via homologous recombination Source: EcoCyc
Keywordsi
Molecular function | DNA-binding, Exonuclease, Helicase, Hydrolase, Nuclease |
Biological process | DNA damage, DNA repair |
Ligand | ATP-binding, Nucleotide-binding |
Enzyme and pathway databases
BioCyci | EcoCyc:EG10826-MONOMER MetaCyc:EG10826-MONOMER |
BRENDAi | 3.1.11.5, 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 |
Organismi | Escherichia coli (strain K12) |
Taxonomic identifieri | 83333 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › |
Proteomesi |
|
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 key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 177 | K → 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 Publications | 1 |
Chemistry databases
ChEMBLi | CHEMBL2095232 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000087115 | 1 – 608 | RecBCD enzyme subunit RecDAdd BLAST | 608 |
Proteomic databases
jPOSTi | P04993 |
PaxDbi | P04993 |
PRIDEi | P04993 |
Interactioni
Subunit structurei
Heterotrimer of RecB, RecC and RecD. All subunits contribute to DNA-binding.
UniRule annotation4 PublicationsProtein-protein interaction databases
BioGRIDi | 4260684, 132 interactors |
ComplexPortali | CPX-2197, Exodeoxyribonuclease V complex |
DIPi | DIP-10651N |
IntActi | P04993, 13 interactors |
MINTi | P04993 |
STRINGi | 511145.b2819 |
Chemistry databases
BindingDBi | P04993 |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | P04993 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | P04993 |
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
eggNOGi | COG0507, Bacteria |
HOGENOMi | CLU_007524_1_2_6 |
InParanoidi | P04993 |
PhylomeDBi | P04993 |
Family and domain databases
Gene3Di | 1.10.10.1020, 1 hit |
HAMAPi | MF_01487, RecD, 1 hit |
InterProi | View protein in InterPro IPR003593, AAA+_ATPase IPR027417, P-loop_NTPase IPR006344, RecD IPR041851, RecD_N IPR027785, UvrD-like_helicase_C |
Pfami | View protein in Pfam PF13538, UvrD_C_2, 1 hit |
SMARTi | View protein in SMART SM00382, AAA, 1 hit |
SUPFAMi | SSF52540, SSF52540, 2 hits |
TIGRFAMsi | TIGR01447, recD, 1 hit |
i Sequence
Sequence statusi: Complete.
P04993-1 [UniParc]FASTAAdd to basket
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
Experimental Info
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Sequence conflicti | 247 – 248 | QP → HR in CAA28253 (PubMed:3537961).Curated | 2 | |
Sequence conflicti | 306 | A → V in CAA28253 (PubMed:3537961).Curated | 1 | |
Sequence conflicti | 390 | F → L in CAA28253 (PubMed:3537961).Curated | 1 |
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 |
PIRi | D65064, NCECXF |
RefSeqi | NP_417296.1, NC_000913.3 WP_000775955.1, NZ_LN832404.1 |
Genome annotation databases
EnsemblBacteriai | AAC75858; AAC75858; b2819 BAE76888; BAE76888; BAE76888 |
GeneIDi | 947287 |
KEGGi | ecj:JW2787 eco:b2819 |
PATRICi | fig|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 |
PIRi | D65064, NCECXF |
RefSeqi | NP_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 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 | [»] | |
5LD2 | electron microscopy | 3.83 | D | 2-608 | [»] | |
5MBV | electron microscopy | 3.80 | D | 2-608 | [»] | |
6SJB | electron microscopy | 3.70 | D | 1-608 | [»] | |
6SJE | electron microscopy | 4.10 | D | 1-608 | [»] | |
6SJF | electron microscopy | 3.90 | D | 1-608 | [»] | |
6SJG | electron microscopy | 3.80 | D | 1-608 | [»] | |
6T2U | electron microscopy | 3.60 | D | 1-608 | [»] | |
6T2V | electron microscopy | 3.80 | D | 1-608 | [»] | |
SMRi | P04993 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 4260684, 132 interactors |
ComplexPortali | CPX-2197, Exodeoxyribonuclease V complex |
DIPi | DIP-10651N |
IntActi | P04993, 13 interactors |
MINTi | P04993 |
STRINGi | 511145.b2819 |
Chemistry databases
BindingDBi | P04993 |
ChEMBLi | CHEMBL2095232 |
Proteomic databases
jPOSTi | P04993 |
PaxDbi | P04993 |
PRIDEi | P04993 |
Genome annotation databases
EnsemblBacteriai | AAC75858; AAC75858; b2819 BAE76888; BAE76888; BAE76888 |
GeneIDi | 947287 |
KEGGi | ecj:JW2787 eco:b2819 |
PATRICi | fig|1411691.4.peg.3917 |
Organism-specific databases
EchoBASEi | EB0819 |
Phylogenomic databases
eggNOGi | COG0507, Bacteria |
HOGENOMi | CLU_007524_1_2_6 |
InParanoidi | P04993 |
PhylomeDBi | P04993 |
Enzyme and pathway databases
BioCyci | EcoCyc:EG10826-MONOMER MetaCyc:EG10826-MONOMER |
BRENDAi | 3.1.11.5, 2026 |
Miscellaneous databases
EvolutionaryTracei | P04993 |
PROi | PR:P04993 |
Family and domain databases
Gene3Di | 1.10.10.1020, 1 hit |
HAMAPi | MF_01487, RecD, 1 hit |
InterProi | View protein in InterPro IPR003593, AAA+_ATPase IPR027417, P-loop_NTPase IPR006344, RecD IPR041851, RecD_N IPR027785, UvrD-like_helicase_C |
Pfami | View protein in Pfam PF13538, UvrD_C_2, 1 hit |
SMARTi | View protein in SMART SM00382, AAA, 1 hit |
SUPFAMi | SSF52540, SSF52540, 2 hits |
TIGRFAMsi | TIGR01447, recD, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | RECD_ECOLI | |
Accessioni | P04993Primary (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: | December 2, 2020 | |
This is version 175 of the entry and version 2 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Prokaryotic Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Direct protein sequencing, Reference proteomeDocuments
- PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families