Information on EC 3.1.11.5 - exodeoxyribonuclease V

Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
Specify your search results
Mark a special word or phrase in this record:
Select one or more organisms in this record:
Show additional data
Do not include text mining results
Include (text mining) results (more...)
Include results (AMENDA + additional results, but less precise; more...)


The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota

EC NUMBER
COMMENTARY
3.1.11.5
-
RECOMMENDED NAME
GeneOntology No.
exodeoxyribonuclease V
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
Exonucleolytic cleavage (in the presence of ATP) in either 5'- to 3'- or 3'- to 5'-direction to yield 5'-phosphooligonucleotides
show the reaction diagram
preference for double-stranded DNA, possesses DNA-dependent ATPase activity, acts endonucleolytically on single-stranded circular DNA
-
Exonucleolytic cleavage (in the presence of ATP) in either 5'- to 3'- or 3'- to 5'-direction to yield 5'-phosphooligonucleotides
show the reaction diagram
mechanism, The enzyme is an ATP-dependent DNA exonuclease and a helicase, its exonuclease activity is subject to regulation by an octameric nucleotide sequence called chi.
-
Exonucleolytic cleavage (in the presence of ATP) in either 5'- to 3'- or 3'- to 5'-direction to yield 5'-phosphooligonucleotides
show the reaction diagram
The enzyme is involved initiating DNA recombination. The nuclease properties of the enzyme are regulated upon recognition of a specific DNA sequence by the translocating enzyme. This sequence, called chi, corresponds to the octamer 5-GCTGGTGG-3.
-
Exonucleolytic cleavage (in the presence of ATP) in either 5'- to 3'- or 3'- to 5'-direction to yield 5'-phosphooligonucleotides
show the reaction diagram
The enzyme generates 3 single-stranded DNA ends used by RecA for homologous recombination. The exonuclease activity is altered when the enzyme encounters a Chi sequence, 5-GCTGGTGG-3, in double-stranded DNA, an event critical to generation of 3 single-stranded DNA. Chi recognition requires that Chi be flanked by DNA at either end. A specific site for Chi recognition exists on enzyme, which binds Chi with greater affinity than a non-Chi sequence and is probably adjacent to non-specific DNA binding sites.
-
Exonucleolytic cleavage (in the presence of ATP) in either 5'- to 3'- or 3'- to 5'-direction to yield 5'-phosphooligonucleotides
show the reaction diagram
The enzyme is required for homologous recombination and DNA repair, the degradative and recombinational activities of enzyme, as well as its structure, are regulated by a specific DNA sequence called Chi. The recombination requires loading of RecA by RecBCD enzyme and that the RecD subunit inhibits this reaction.
-
Exonucleolytic cleavage (in the presence of ATP) in either 5'- to 3'- or 3'- to 5'-direction to yield 5'-phosphooligonucleotides
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
DNA-dependent ATPase activity
-
-
-
-
hydrolysis of phosphoric ester
-
-
-
-
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
AddAB enzyme
-
-
E. coli ATP-dependent DNase
-
-
-
-
E. coli exonuclease V
-
-
-
-
Escherichia coli exonuclease V
-
-
-
-
Escherichia coli RecBCD
-
-
-
-
Exodeoxyribonuclease V 125 kDa polypeptide
-
-
-
-
Exodeoxyribonuclease V 135 KDA polypeptide
-
-
-
-
Exodeoxyribonuclease V 67 kDa polypeptide
-
-
-
-
exonuclease V
-
-
-
-
exonuclease V
-
-
ExoV
Escherichia coli K12
-
-
-
gene recBC DNase
-
-
-
-
gene RecBC endoenzyme
-
-
-
-
nuclease, exodeoxyribo V
-
-
-
-
PAB2263
Q9V2E8
-
REcB30 protein
-
universal nuclease domain of REcBCD
recBC deoxyribonuclease
-
-
-
-
recBC DNase
-
-
-
-
recBC nuclease
-
-
-
-
RecBCD
P08394 and P04993 and P07648
-
RecBCD DNase
-
-
recBCD enzyme
-
-
-
-
recBCD enzyme
-
-
recBCD enzyme
-
-
recBCD enzyme
-
-
-
RecBCD exonuclease
-
-
RecBCD exonuclease
Escherichia coli JM109
-
-
-
UPF0286 protein PYRAB01260
Q9V2E8
-
CAS REGISTRY NUMBER
COMMENTARY
37350-26-8
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
strains JV28, KOM18, KOM45 and EK6
-
-
Manually annotated by BRENDA team
BL21 strain and BL21-RecD-SBP strain
-
-
Manually annotated by BRENDA team
mutants lacking the recB or recC or recD gene
-
-
Manually annotated by BRENDA team
RecB beta chain and REcD alpha chain and Rec C gamma chain
P08394 and P04993 and P07648
UniProt
Manually annotated by BRENDA team
RecB2109 gene
UniProt
Manually annotated by BRENDA team
recB2109CD mutant
-
-
Manually annotated by BRENDA team
rorA mutant
-
-
Manually annotated by BRENDA team
thermosensitive mutants with thermolabile adenosine 5'-triphosphate-dependent exonucleolytic hydrolysis of duplex DNA
-
-
Manually annotated by BRENDA team
Escherichia coli JM109
-
-
-
Manually annotated by BRENDA team
Escherichia coli K12
K12
-
-
Manually annotated by BRENDA team
Micrococcus luteus
-
-
Manually annotated by BRENDA team
three genes, recC, recB, and recD, in the recCBD operon
-
-
Manually annotated by BRENDA team
three genes, recC, recB, and recD, in the recCBD operon
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
malfunction
-
individual null-mutations of all three genes, recC, recB, and recD, or the deletion of whole recCBD operon of Pseudomonas syringae, lead to growth inhibition at low temperature, and sensitivity to UV and mitomycin C. Viability of the mutant cells drops drastically at 4C, and the mutants accumulate linear chromosomal DNA and shorter DNA fragments in higher amounts compared to 22C
malfunction
-
individual null-mutations of all three genes, recC, recB, and recD, or the deletion of whole recCBD operon of Pseudomonas syringae, lead to growth inhibition at low temperature, and sensitivity to UV and mitomycin C. Viability of the mutant cells drops drastically at 4C, and the mutants accumulate linear chromosomal DNA and shorter DNA fragments in higher amounts compared to 22C
-
physiological function
-
type I DNA restriction/modification systems are oligomeric enzymes capable of switching between a methyltransferase function on hemimethylated host DNA and an endonuclease function on unmethylated foreign DNA. Reuse of the methyltransferase subunits is possible so that restriction proceeds until the restriction subunits are depleted. RecBCD exonuclease halts restriction and does not assist recycling, influence of RecBCD on the EcoKI type I restriction enzyme, overview
physiological function
-
RecD associates with two other proteins RecB and RecC to produce RecBCD enzyme, which is involved in homologous recombination and DNA repair in many bacteria, including Escherichia coli. All three subunits of the RecBCDPs enzyme are essential for DNA repair and growth of Pseudomonas syringae at low temperatures of 4C. The RecD requirement is only a function of the RecBCD complex in the bacterium. The RecBCD pathway protects the Antarctic bacterium from cold-induced DNA damages, and is critically dependent on the helicase activities of both RecB and RecD subunits, but not on the nuclease of RecBCDPs enzyme
physiological function
Escherichia coli JM109
-
type I DNA restriction/modification systems are oligomeric enzymes capable of switching between a methyltransferase function on hemimethylated host DNA and an endonuclease function on unmethylated foreign DNA. Reuse of the methyltransferase subunits is possible so that restriction proceeds until the restriction subunits are depleted. RecBCD exonuclease halts restriction and does not assist recycling, influence of RecBCD on the EcoKI type I restriction enzyme, overview
-
physiological function
-
RecD associates with two other proteins RecB and RecC to produce RecBCD enzyme, which is involved in homologous recombination and DNA repair in many bacteria, including Escherichia coli. All three subunits of the RecBCDPs enzyme are essential for DNA repair and growth of Pseudomonas syringae at low temperatures of 4C. The RecD requirement is only a function of the RecBCD complex in the bacterium. The RecBCD pathway protects the Antarctic bacterium from cold-induced DNA damages, and is critically dependent on the helicase activities of both RecB and RecD subunits, but not on the nuclease of RecBCDPs enzyme
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
3',5'-cyclic AMP
-
less effective than ATP
5'-AMP
-
less effective than ATP
adenine
-
less effective than ATP
adenosine
-
less effective than ATP
ADP
-
less effective than ATP
Bovine serum albumin
-
2-3fold stimulation; required for endonuclaes activity
-
Bovine serum albumin
-
2-3fold stimulation
-
CTP
-
less effective than ATP
dATP
-
nearly as effective as ATP
dCTP
-
less effective than ATP
GTP
-
less effective than ATP
NaCl
-
ATP molecules hydrolyzed per base pair unwound slightly increased
RNA-DNA hybrid
-
activates ATPase only
-
S-adenosylmethionine
-
less effective than ATP
TTP
-
less effective than ATP
UTP
-
less effective than ATP
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
1.4
-
34-mer ssDNA
-
25C
-
250
-
ATP
-
DNA-unwinding activity
740
-
ATP
-
DNA-dependent ATPase activity
3.7
-
ds-DNA
-
25C
-
additional information
-
additional information
-
The corrected unwinding rate is 443 base pairs 1/sec, which is due to a single molecule of enzyme that bound to the free double-stranded DNA end opposite the bead, and both translocates and unwinds the DNA in an ATP-dependent manner once the DNA entered the ATP channel. The rate of unwinding increases with increasing ATP concentration and increasing temperature
-
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
0.024
-
-
-
pH RANGE
pH RANGE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
30
-
-
assay at
TEMPERATURE RANGE
TEMPERATURE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
23
37
-
The rate of unwinding in 1 mM ATP increases twofold when the temperature is raised from 23C to 37C.
25
37
-
15000 base pairs of DNA per min at 25C; 55800 base pairs of DNA per min at 37C
30
43
-
pH 9.0, wild type, at 43C fourfold higher activity than at 30C
additional information
-
-
by altering the cultivation temperature (37C) of the cells to a moderately lower range (20-34C), dramatically reduces the linear DNA degradation activity of RecD
PDB
SCOP
CATH
ORGANISM
Escherichia coli (strain K12)
Escherichia coli (strain K12)
TEMPERATURE STABILITY
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
42
-
-
complete stable in presence of DNA for 40 min; faster inactivation in presence of ATP
GENERAL STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
DNA stabilizes against thermal denaturation
-
RecBC enzyme more instable than the recBCD enzyme
-
stable during purification except steps requiring salt elution
-
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
-20C, purified enzyme RecBC, 1 year, 80% loss of activity
-
-20C, purified enzyme RecBCD, 1 year, 10%-20% loss of activity
-
-20C, purified enzyme, 1 month, 35% loss of activity
-
-20C, purified enzyme, 7 months, 80% loss of activity
-
-70C, purified enzyme, 6 weeks, 0% loss of activity
-
0C, Tris, MgCl2, EDTA, mercaptoethanol, 1 d, 5-10% loss of activity
-
4C, RecC, stable for several months
-
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
D1067A
-
The mutation in the carboxyl-terminal nuclease domain of the RecB subunit abolishes nuclease activity on both single- and double-stranded DNA but the mutant enzyme is active as helicase. The mutant is unable to produce chi-specific fragments from either strand of a chi-containing double-stranded DNA substrate.
D1067A
-
chi is not a hot-spot for recombination in the mutant, the mutant is sligthtly defective for recombinational repair
D1080A
-
chi is not a hot-spot for recombination in the mutant, the mutant is sligthtly defective for recombinational repair
D1080A
-
Comparison: recB(D1080A)CD is recombinant-deficient, and sensitive to DNA damaging agents, and the purified enzyme failed to load RecA during DNA winding. recB(D1080A)C is recombinant-proficient and resistant to DNA damaging agents, and the mutant is active RecA loading assay.
K1082A
-
chi is not a hot-spot for recombination in the mutant, the mutant is sligthtly defective for recombinational repair
K1082Q
-
The mutation in the carboxyl-terminal nuclease domain of the RecB subunit abolishes nuclease activity on both single- and double-stranded DNA but the mutant enzyme is active as helicase. The mutant is unable to produce chi-specific fragments from either strand of a chi-containing double-stranded DNA substrate.
Y1081A
-
The mutation in the carboxyl-terminal nuclease domain of the RecB subunit exhibits substantial nuclease activity.
Y1081F
-
The mutation in the carboxyl-terminal nuclease domain of the RecB subunit exhibits essentially wild-type levels of activity.
Y1114A
-
The mutation in the carboxyl-terminal nuclease domain of the RecB subunit exhibits substantial nuclease activity.
Y1114F
-
The mutation in the carboxyl-terminal nuclease domain of the RecB subunit exhibits essentially wild-type levels of activity.
D1067A
Escherichia coli K12
-
chi is not a hot-spot for recombination in the mutant, the mutant is sligthtly defective for recombinational repair
-
D1080A
Escherichia coli K12
-
chi is not a hot-spot for recombination in the mutant, the mutant is sligthtly defective for recombinational repair
-
K1082A
Escherichia coli K12
-
chi is not a hot-spot for recombination in the mutant, the mutant is sligthtly defective for recombinational repair
-
D1118A
-
site-directed mutagenesis, inactivation in the nuclease center of RecB
K229Q
-
site-directed mutagenesis, inactivation of the ATPase active site of RecD
D1118A
-
site-directed mutagenesis, inactivation in the nuclease center of RecB
-
K229Q
-
site-directed mutagenesis, inactivation of the ATPase active site of RecD
-
K177Q
-
involved in ATP binding site of the recD protein
additional information
-
recBC1010D, recBC1041D and recBCD1013 mutants have less than 0.2% of the exonuclease activity of wild-type enzyme. recBC1010D and recBC1041D produce RecD but fail to assemble it into holoenzyme
additional information
P08394
the mutant RecB2109CD degrades the double-stranded DNA primarily in the 5 to 3 direction, producing processed double-stranded DNA with a 3-terminal overhang, the mutant is unable to coordinate the loading of RecA protein onto the single-stranded DNA produced, this inability can be responsible for recB2109 recombination defect observed in vivo
additional information
-
RecB mutants that cannot bind or hydrolyze ATP are completely defective for DNA recombination
additional information
-
in mutants carrying either recB2109 or recD1903, which do not exhibit significant nuclease activities, the prophage progressively loses its capacity for both site-specific and general recombination
additional information
-
the recombination deficiency of the RecBC1004D-chi interaction can be overcome by the enhanced ability of RecA730 to assemble on single-stranded DNA in vitro and in vivo
K29Q
-
site-directed mutagenesis, inactivation of the ATPase active site of RecB
additional information
-
disruption of genes in the recCBD operon and creation of DELTArecC, DELTArecB, DELTArecD, and DELTArecCBD strains of Pseudomonas syringae Lz4W
K29Q
-
site-directed mutagenesis, inactivation of the ATPase active site of RecB
-
additional information
-
disruption of genes in the recCBD operon and creation of DELTArecC, DELTArecB, DELTArecD, and DELTArecCBD strains of Pseudomonas syringae Lz4W
-