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Protein

RecBCD enzyme subunit RecB

Gene

recB

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. 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

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 keyPosition(s)DescriptionActionsGraphical viewLength
Metal bindingi956Magnesium; via tele nitrogenCurated1
Metal bindingi1067MagnesiumCurated1
Active sitei1080For nuclease activity2 Publications1
Metal bindingi1080MagnesiumCurated1
Metal bindingi1081Magnesium; via carbonyl oxygenCurated1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi23 – 30ATP8
DNA bindingi252 – 2543
DNA bindingi511 – 5122
DNA bindingi560 – 5612
DNA bindingi7611

GO - Molecular functioni

GO - Biological processi

  • clearance of foreign intracellular DNA Source: UniProtKB
  • DNA recombination Source: EcoCyc
  • double-strand break repair via homologous recombination Source: EcoCyc
  • response to radiation Source: EcoCyc

Keywordsi

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

Enzyme and pathway databases

BioCyciEcoCyc:EG10824-MONOMER
MetaCyc:EG10824-MONOMER
BRENDAi3.1.11.5 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
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10824 recB

Subcellular locationi

GO - Cellular componenti

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 keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi29K → Q: Subunit loses ATPase and 3'-5' helicase activity, holoenzyme has 3-5 fold less helicase activity, 20-fold less processivity. 3 Publications1
Mutagenesisi803Y → 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 Publication1
Mutagenesisi804V → 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 Publication1
Mutagenesisi807T → I in recB-2109; absence of nuclease modification at Chi sites. 1 Publication1
Mutagenesisi1067D → A: Subunit loses nuclease activity. 1 Publication1
Mutagenesisi1080D → 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 Publications1

Chemistry databases

ChEMBLiCHEMBL2095232

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00001020462 – 1180RecBCD enzyme subunit RecBAdd BLAST1179

Proteomic databases

PaxDbiP08394
PRIDEiP08394

Interactioni

Subunit structurei

Heterotrimer of RecB, RecC and RecD. All subunits contribute to DNA-binding. The C-terminus interacts with RecA (PubMed:16483938). Interacts with YgbT (Cas1) (PubMed:21219465).8 Publications

Protein-protein interaction databases

BioGridi4262307, 585 interactors
ComplexPortaliCPX-2197 Exodeoxyribonuclease V complex
DIPiDIP-540N
IntActiP08394, 20 interactors
MINTiP08394
STRINGi316385.ECDH10B_2990

Structurei

Secondary structure

11180
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

ProteinModelPortaliP08394
SMRiP08394
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP08394

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini2 – 450UvrD-like helicase ATP-bindingUniRule annotationAdd BLAST449
Domaini480 – 746UvrD-like helicase C-terminalUniRule annotationAdd BLAST267

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni2 – 927ATPase, DNA-binding and helicase activity, interacts with RecCAdd BLAST926
Regioni928 – 1180Nuclease activity, interacts with RecD and RecAAdd BLAST253

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

Belongs to the helicase family. UvrD subfamily.UniRule annotation

Phylogenomic databases

eggNOGiENOG4107QKA Bacteria
COG1074 LUCA
HOGENOMiHOG000258330
InParanoidiP08394
KOiK03582
PhylomeDBiP08394

Family and domain databases

Gene3Di3.90.320.10, 1 hit
HAMAPiMF_01485 RecB, 1 hit
InterProiView 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
PANTHERiPTHR11070 PTHR11070, 1 hit
PTHR11070:SF23 PTHR11070:SF23, 1 hit
PfamiView protein in Pfam
PF12705 PDDEXK_1, 1 hit
PF00580 UvrD-helicase, 1 hit
PF13361 UvrD_C, 1 hit
SUPFAMiSSF52540 SSF52540, 1 hit
SSF52980 SSF52980, 1 hit
TIGRFAMsiTIGR00609 recB, 1 hit
PROSITEiView protein in PROSITE
PS51198 UVRD_HELICASE_ATP_BIND, 1 hit
PS51217 UVRD_HELICASE_CTER, 1 hit

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P08394-1 [UniParc]FASTAAdd to basket
« Hide
        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
Length:1,180
Mass (Da):133,959
Last modified:August 1, 1988 - v1
Checksum:iF9AC331808E8F281
GO

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
PIRiA25532 NCECX5
RefSeqiNP_417297.1, NC_000913.3
WP_001285993.1, NZ_LN832404.1

Genome annotation databases

EnsemblBacteriaiAAC75859; AAC75859; b2820
BAE76889; BAE76889; BAE76889
GeneIDi947286
KEGGiecj:JW2788
eco:b2820
PATRICifig|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
PIRiA25532 NCECX5
RefSeqiNP_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 entryMethodResolution (Å)ChainPositionsPDBsum
1W36X-ray3.10B/E1-1180[»]
3K70X-ray3.59B/E1-1180[»]
5LD2electron microscopy3.83B1-1180[»]
5MBVelectron microscopy3.80B1-1180[»]
ProteinModelPortaliP08394
SMRiP08394
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262307, 585 interactors
ComplexPortaliCPX-2197 Exodeoxyribonuclease V complex
DIPiDIP-540N
IntActiP08394, 20 interactors
MINTiP08394
STRINGi316385.ECDH10B_2990

Chemistry databases

ChEMBLiCHEMBL2095232

Proteomic databases

PaxDbiP08394
PRIDEiP08394

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75859; AAC75859; b2820
BAE76889; BAE76889; BAE76889
GeneIDi947286
KEGGiecj:JW2788
eco:b2820
PATRICifig|1411691.4.peg.3916

Organism-specific databases

EchoBASEiEB0817
EcoGeneiEG10824 recB

Phylogenomic databases

eggNOGiENOG4107QKA Bacteria
COG1074 LUCA
HOGENOMiHOG000258330
InParanoidiP08394
KOiK03582
PhylomeDBiP08394

Enzyme and pathway databases

BioCyciEcoCyc:EG10824-MONOMER
MetaCyc:EG10824-MONOMER
BRENDAi3.1.11.5 2026

Miscellaneous databases

EvolutionaryTraceiP08394
PROiPR:P08394

Family and domain databases

Gene3Di3.90.320.10, 1 hit
HAMAPiMF_01485 RecB, 1 hit
InterProiView 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
PANTHERiPTHR11070 PTHR11070, 1 hit
PTHR11070:SF23 PTHR11070:SF23, 1 hit
PfamiView protein in Pfam
PF12705 PDDEXK_1, 1 hit
PF00580 UvrD-helicase, 1 hit
PF13361 UvrD_C, 1 hit
SUPFAMiSSF52540 SSF52540, 1 hit
SSF52980 SSF52980, 1 hit
TIGRFAMsiTIGR00609 recB, 1 hit
PROSITEiView protein in PROSITE
PS51198 UVRD_HELICASE_ATP_BIND, 1 hit
PS51217 UVRD_HELICASE_CTER, 1 hit
ProtoNetiSearch...

Entry informationi

Entry nameiRECB_ECOLI
AccessioniPrimary (citable) accession number: P08394
Secondary accession number(s): Q2MA17
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1988
Last sequence update: August 1, 1988
Last modified: November 7, 2018
This is version 165 of the entry and version 1 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
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