UniProtKB - P08394 (RECB_ECOLI)
Protein
RecBCD enzyme subunit RecB
Gene
recB
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. Holoenzyme degrades any linearized DNA that is unable to undergo homologous recombination (PubMed:4562392, PubMed:4552016, PubMed:123277). In the holoenzyme this subunit contributes ATPase, 3'-5' helicase, exonuclease activity and loads RecA onto ssDNA. The RecBC complex requires the RecD subunit for nuclease activity, but can translocate along ssDNA in both directions.22 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
Cofactori
Mg2+UniRule annotationCurated3 PublicationsNote: Magnesium is required for both helicase and nuclease activity; its relative concentration alters helicase speed and nuclease activity in a complicated fashion.UniRule annotationCurated3 Publications
Activity regulationi
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).2 Publications
Sites
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Metal bindingi | 956 | Magnesium; via tele nitrogenCurated | 1 | |
Metal bindingi | 1067 | MagnesiumCurated | 1 | |
Active sitei | 1080 | For nuclease activity2 Publications | 1 | |
Metal bindingi | 1080 | MagnesiumCurated | 1 | |
Metal bindingi | 1081 | Magnesium; via carbonyl oxygenCurated | 1 |
Regions
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Nucleotide bindingi | 23 – 30 | ATP | 8 | |
DNA bindingi | 252 – 254 | 3 | ||
DNA bindingi | 511 – 512 | 2 | ||
DNA bindingi | 560 – 561 | 2 | ||
DNA bindingi | 761 | 1 |
GO - Molecular functioni
- 3'-5' DNA helicase activity Source: GO_Central
- ATP binding Source: EcoCyc
- DNA binding Source: UniProtKB-UniRule
- DNA-dependent ATPase activity Source: EcoCyc
- DNA helicase activity Source: EcoCyc
- DNA translocase activity Source: EcoCyc
- endodeoxyribonuclease activity Source: EcoCyc
- exodeoxyribonuclease V activity Source: EcoCyc
- magnesium ion binding Source: UniProtKB-UniRule
GO - Biological processi
- clearance of foreign intracellular DNA Source: UniProtKB
- DNA recombination Source: EcoCyc
- DNA repair Source: GO_Central
- double-strand break repair via homologous recombination Source: EcoCyc
- recombinational repair Source: GO_Central
- response to radiation Source: EcoCyc
Keywordsi
Molecular function | DNA-binding, Exonuclease, Helicase, Hydrolase, Nuclease |
Biological process | DNA damage, DNA repair |
Ligand | ATP-binding, Magnesium, Metal-binding, Nucleotide-binding |
Enzyme and pathway databases
BioCyci | EcoCyc:EG10824-MONOMER MetaCyc:EG10824-MONOMER |
BRENDAi | 3.1.11.5, 2026 |
Names & Taxonomyi
Protein namesi | Recommended name: RecBCD enzyme subunit RecBUniRule annotation (EC:3.1.11.5UniRule annotation)Alternative name(s): Exodeoxyribonuclease V 135 kDa polypeptide Exodeoxyribonuclease V beta chain Exonuclease V subunit RecBUniRule annotation Short name: ExoV subunit RecBUniRule annotation Helicase/nuclease RecBCD subunit RecBUniRule annotation |
Gene namesi | Name:recBUniRule annotation Synonyms:ior, rorA Ordered Locus Names:b2820, JW2788 |
Organismi | Escherichia coli (strain K12) |
Taxonomic identifieri | 83333 [NCBI] |
Taxonomic lineagei | Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacterales › Enterobacteriaceae › Escherichia › |
Proteomesi |
|
Subcellular locationi
GO - Cellular componenti
- cytosol Source: GO_Central
- exodeoxyribonuclease V complex Source: EcoCyc
Pathology & Biotechi
Disruption phenotypei
Decreased degradation of DNA with free ends that is unable to undergo homologous recombination, which can fortuitously lead to more efficient viral infection (PubMed:4562392, PubMed:123277). Cells are deficient in DNA recombination repair and have increased sensitivity to UV light. The cultures have many inviable cells.3 Publications
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 29 | K → Q: Subunit loses ATPase and 3'-5' helicase activity, holoenzyme has 3-5 fold less helicase activity, 20-fold less processivity. 3 Publications | 1 | |
Mutagenesisi | 803 | Y → H: Large decrease in recombination, loss of Chi hotspot activity, decreased RecB helicase rate, retains nuclease activity but not Chi-sequence specificity, does not load RecA. 1 Publication | 1 | |
Mutagenesisi | 804 | V → E: Large decrease in recombination, loss of Chi hotspot activity, decreased RecB helicase rate, retains nuclease activity but not Chi-sequence specificity, does not load RecA. 1 Publication | 1 | |
Mutagenesisi | 807 | T → I in recB-2109; absence of nuclease modification at Chi sites. 1 Publication | 1 | |
Mutagenesisi | 1067 | D → A: Subunit loses nuclease activity. 1 Publication | 1 | |
Mutagenesisi | 1080 | D → A: Loss of holoenzyme nuclease activity, retains full helicase activity, does not act at Chi, no loading of RecA on ssDNA and no recombinational repair. 3 Publications | 1 |
Chemistry databases
ChEMBLi | CHEMBL2095232 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Initiator methioninei | Removed1 Publication | |||
ChainiPRO_0000102046 | 2 – 1180 | RecBCD enzyme subunit RecBAdd BLAST | 1179 |
Proteomic databases
jPOSTi | P08394 |
PaxDbi | P08394 |
PRIDEi | P08394 |
Interactioni
Subunit structurei
Protein-protein interaction databases
BioGRIDi | 4262307, 585 interactors 851614, 3 interactors |
ComplexPortali | CPX-2197, Exodeoxyribonuclease V complex |
DIPi | DIP-540N |
IntActi | P08394, 20 interactors |
MINTi | P08394 |
STRINGi | 511145.b2820 |
Structurei
Secondary structure
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details3D structure databases
SMRi | P08394 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | P08394 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Domaini | 2 – 450 | UvrD-like helicase ATP-bindingUniRule annotationAdd BLAST | 449 | |
Domaini | 480 – 746 | UvrD-like helicase C-terminalUniRule annotationAdd BLAST | 267 |
Region
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Regioni | 2 – 927 | ATPase, DNA-binding and helicase activity, interacts with RecCAdd BLAST | 926 | |
Regioni | 928 – 1180 | Nuclease activity, interacts with RecD and RecAAdd BLAST | 253 |
Domaini
The N-terminal DNA-binding domain (residues 1-929) is a ssDNA-dependent ATPase and has ATP-dependent 3'-5' helicase function; both are stimulated in the presence of RecC, suggesting this domain interacts with RecC. Holoenzyme reconstituted with this RecB N-terminal fragment has no nuclease activity (PubMed:9448271). The C-terminal domain (residues 928-1180) has weak ssDNA endonuclease activity as an isolated fragment (PubMed:9790841) (PubMed:10518611). RecD probably interacts with this domain. The C-terminal domain interacts with RecA, facilitating its loading onto ssDNA. Interaction is decreased by ATP (PubMed:16483938).4 Publications
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
Phylogenomic databases
eggNOGi | COG1074, Bacteria |
HOGENOMi | CLU_001114_6_0_6 |
InParanoidi | P08394 |
PhylomeDBi | P08394 |
Family and domain databases
Gene3Di | 3.90.320.10, 1 hit |
HAMAPi | MF_01485, RecB, 1 hit |
InterProi | View protein in InterPro IPR014017, DNA_helicase_UvrD-like_C IPR000212, DNA_helicase_UvrD/REP IPR011604, Exonuc_phg/RecB_C IPR027417, P-loop_NTPase IPR038726, PDDEXK_AddAB-type IPR004586, RecB IPR011335, Restrct_endonuc-II-like IPR014016, UvrD-like_ATP-bd IPR034739, UvrD/AddA_N |
PANTHERi | PTHR11070, PTHR11070, 1 hit PTHR11070:SF23, PTHR11070:SF23, 1 hit |
Pfami | View protein in Pfam PF12705, PDDEXK_1, 1 hit PF00580, UvrD-helicase, 1 hit PF13361, UvrD_C, 1 hit |
SUPFAMi | SSF52540, SSF52540, 1 hit SSF52980, SSF52980, 1 hit |
TIGRFAMsi | TIGR00609, recB, 1 hit |
PROSITEi | View protein in PROSITE PS51198, UVRD_HELICASE_ATP_BIND, 1 hit PS51217, UVRD_HELICASE_CTER, 1 hit |
i Sequence
Sequence statusi: Complete.
: The displayed sequence is further processed into a mature form. Sequence processingi
P08394-1 [UniParc]FASTAAdd to basket
10 20 30 40 50
MSDVAETLDP LRLPLQGERL IEASAGTGKT FTIAALYLRL LLGLGGSAAF
60 70 80 90 100
PRPLTVEELL VVTFTEAATA ELRGRIRSNI HELRIACLRE TTDNPLYERL
110 120 130 140 150
LEEIDDKAQA AQWLLLAERQ MDEAAVFTIH GFCQRMLNLN AFESGMLFEQ
160 170 180 190 200
QLIEDESLLR YQACADFWRR HCYPLPREIA QVVFETWKGP QALLRDINRY
210 220 230 240 250
LQGEAPVIKA PPPDDETLAS RHAQIVARID TVKQQWRDAV GELDALIESS
260 270 280 290 300
GIDRRKFNRS NQAKWIDKIS AWAEEETNSY QLPESLEKFS QRFLEDRTKA
310 320 330 340 350
GGETPRHPLF EAIDQLLAEP LSIRDLVITR ALAEIRETVA REKRRRGELG
360 370 380 390 400
FDDMLSRLDS ALRSESGEVL AAAIRTRFPV AMIDEFQDTD PQQYRIFRRI
410 420 430 440 450
WHHQPETALL LIGDPKQAIY AFRGADIFTY MKARSEVHAH YTLDTNWRSA
460 470 480 490 500
PGMVNSVNKL FSQTDDAFMF REIPFIPVKS AGKNQALRFV FKGETQPAMK
510 520 530 540 550
MWLMEGESCG VGDYQSTMAQ VCAAQIRDWL QAGQRGEALL MNGDDARPVR
560 570 580 590 600
ASDISVLVRS RQEAAQVRDA LTLLEIPSVY LSNRDSVFET LEAQEMLWLL
610 620 630 640 650
QAVMTPEREN TLRSALATSM MGLNALDIET LNNDEHAWDV VVEEFDGYRQ
660 670 680 690 700
IWRKRGVMPM LRALMSARNI AENLLATAGG ERRLTDILHI SELLQEAGTQ
710 720 730 740 750
LESEHALVRW LSQHILEPDS NASSQQMRLE SDKHLVQIVT IHKSKGLEYP
760 770 780 790 800
LVWLPFITNF RVQEQAFYHD RHSFEAVLDL NAAPESVDLA EAERLAEDLR
810 820 830 840 850
LLYVALTRSV WHCSLGVAPL VRRRGDKKGD TDVHQSALGR LLQKGEPQDA
860 870 880 890 900
AGLRTCIEAL CDDDIAWQTA QTGDNQPWQV NDVSTAELNA KTLQRLPGDN
910 920 930 940 950
WRVTSYSGLQ QRGHGIAQDL MPRLDVDAAG VASVVEEPTL TPHQFPRGAS
960 970 980 990 1000
PGTFLHSLFE DLDFTQPVDP NWVREKLELG GFESQWEPVL TEWITAVLQA
1010 1020 1030 1040 1050
PLNETGVSLS QLSARNKQVE MEFYLPISEP LIASQLDTLI RQFDPLSAGC
1060 1070 1080 1090 1100
PPLEFMQVRG MLKGFIDLVF RHEGRYYLLD YKSNWLGEDS SAYTQQAMAA
1110 1120 1130 1140 1150
AMQAHRYDLQ YQLYTLALHR YLRHRIADYD YEHHFGGVIY LFLRGVDKEH
1160 1170 1180
PQQGIYTTRP NAGLIALMDE MFAGMTLEEA
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | X04581 Genomic DNA Translation: CAA28250.1 AF179304 Genomic DNA Translation: AAD56369.1 U29581 Genomic DNA Translation: AAB40467.1 U00096 Genomic DNA Translation: AAC75859.1 AP009048 Genomic DNA Translation: BAE76889.1 X06227 Genomic DNA Translation: CAA29577.1 X04582 Genomic DNA Translation: CAA28252.1 |
PIRi | A25532, NCECX5 |
RefSeqi | NP_417297.1, NC_000913.3 WP_001285993.1, NZ_LN832404.1 |
Genome annotation databases
EnsemblBacteriai | AAC75859; AAC75859; b2820 BAE76889; BAE76889; BAE76889 |
GeneIDi | 947286 |
KEGGi | ecj:JW2788 eco:b2820 |
PATRICi | fig|1411691.4.peg.3916 |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | X04581 Genomic DNA Translation: CAA28250.1 AF179304 Genomic DNA Translation: AAD56369.1 U29581 Genomic DNA Translation: AAB40467.1 U00096 Genomic DNA Translation: AAC75859.1 AP009048 Genomic DNA Translation: BAE76889.1 X06227 Genomic DNA Translation: CAA29577.1 X04582 Genomic DNA Translation: CAA28252.1 |
PIRi | A25532, NCECX5 |
RefSeqi | NP_417297.1, NC_000913.3 WP_001285993.1, 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 | B/E | 1-1180 | [»] | |
3K70 | X-ray | 3.59 | B/E | 1-1180 | [»] | |
5LD2 | electron microscopy | 3.83 | B | 1-1180 | [»] | |
5MBV | electron microscopy | 3.80 | B | 1-1180 | [»] | |
6SJB | electron microscopy | 3.70 | B | 1-1180 | [»] | |
6SJE | electron microscopy | 4.10 | B | 1-1180 | [»] | |
6SJF | electron microscopy | 3.90 | B | 1-1180 | [»] | |
6SJG | electron microscopy | 3.80 | B | 1-1180 | [»] | |
6T2U | electron microscopy | 3.60 | B | 1-1180 | [»] | |
6T2V | electron microscopy | 3.80 | B | 1-1180 | [»] | |
SMRi | P08394 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 4262307, 585 interactors 851614, 3 interactors |
ComplexPortali | CPX-2197, Exodeoxyribonuclease V complex |
DIPi | DIP-540N |
IntActi | P08394, 20 interactors |
MINTi | P08394 |
STRINGi | 511145.b2820 |
Chemistry databases
ChEMBLi | CHEMBL2095232 |
Proteomic databases
jPOSTi | P08394 |
PaxDbi | P08394 |
PRIDEi | P08394 |
Genome annotation databases
EnsemblBacteriai | AAC75859; AAC75859; b2820 BAE76889; BAE76889; BAE76889 |
GeneIDi | 947286 |
KEGGi | ecj:JW2788 eco:b2820 |
PATRICi | fig|1411691.4.peg.3916 |
Organism-specific databases
EchoBASEi | EB0817 |
Phylogenomic databases
eggNOGi | COG1074, Bacteria |
HOGENOMi | CLU_001114_6_0_6 |
InParanoidi | P08394 |
PhylomeDBi | P08394 |
Enzyme and pathway databases
BioCyci | EcoCyc:EG10824-MONOMER MetaCyc:EG10824-MONOMER |
BRENDAi | 3.1.11.5, 2026 |
Miscellaneous databases
EvolutionaryTracei | P08394 |
PROi | PR:P08394 |
Family and domain databases
Gene3Di | 3.90.320.10, 1 hit |
HAMAPi | MF_01485, RecB, 1 hit |
InterProi | View protein in InterPro IPR014017, DNA_helicase_UvrD-like_C IPR000212, DNA_helicase_UvrD/REP IPR011604, Exonuc_phg/RecB_C IPR027417, P-loop_NTPase IPR038726, PDDEXK_AddAB-type IPR004586, RecB IPR011335, Restrct_endonuc-II-like IPR014016, UvrD-like_ATP-bd IPR034739, UvrD/AddA_N |
PANTHERi | PTHR11070, PTHR11070, 1 hit PTHR11070:SF23, PTHR11070:SF23, 1 hit |
Pfami | View protein in Pfam PF12705, PDDEXK_1, 1 hit PF00580, UvrD-helicase, 1 hit PF13361, UvrD_C, 1 hit |
SUPFAMi | SSF52540, SSF52540, 1 hit SSF52980, SSF52980, 1 hit |
TIGRFAMsi | TIGR00609, recB, 1 hit |
PROSITEi | View protein in PROSITE PS51198, UVRD_HELICASE_ATP_BIND, 1 hit PS51217, UVRD_HELICASE_CTER, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | RECB_ECOLI | |
Accessioni | P08394Primary (citable) accession number: P08394 Secondary accession number(s): Q2MA17 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | August 1, 1988 |
Last sequence update: | August 1, 1988 | |
Last modified: | December 2, 2020 | |
This is version 182 of the entry and version 1 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