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Enzyme Nomenclature
Information on EC 3.1.11.3 - exodeoxyribonuclease (lambda-induced)
for references in articles please use BRENDA:EC3.1.11.3
Word Map on EC 3.1.11.3
- 3.1.11.3
-
single-stranded
-
double-stranded
-
endonuclease
-
polymerases
-
proofreading
-
mismatch
-
duplex
- bacteriophage
-
helicase
-
excision
-
fidelity
-
exonucleolytic
-
nick
-
nucleases
- fork
-
werner
-
klenow
- ssdna
- dntp
-
anneal
-
mispairs
-
telomere
-
misincorporation
- polynucleotide
-
recbcd
- deoxynucleoside
-
unwind
-
abasic
-
overhang
-
okazaki
-
deadenylation
-
3'-terminus
-
structure-specific
-
nucleolytic
- primase
- exoribonuclease
-
apurinic
- aphidicolin
-
translesion
-
decapping
-
template-primer
-
primer-template
- cidofovir
-
g-quadruplexes
-
5'-phosphorylated
-
progeroid
- pnpase
-
replisome
-
aptasensor
- analysis
- synthesis
-
single-strand-specific
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Specify your search results
The enzyme appears in viruses and cellular organisms
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EC NUMBER 
COMMENTARY 
3.1.11.3
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RECOMMENDED NAME
GeneOntology No.
exodeoxyribonuclease (lambda-induced)
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 5'-phosphates
-
-
-
-
exonucleolytic cleavage in the 5'- to 3'-direction to yield nucleoside 5'-phosphates
lambda exonuclease uses a classic two-metal mechanism
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of phosphoric ester
-
-
-
-
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CAS REGISTRY NUMBER
COMMENTARY
37288-28-1
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Escherichia coli infected with phage lambda only
133972, 133978, 133979, 133980, 133981, 133983, 133984, 133985, 133986, 133987, 133988, 133989, 133993
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-
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133972, 133978, 133979, 133983, 133984, 133986, 133987, 133989, 133992, 133993, 713754, 716778, 728851, 728953
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defective lambda mutant T11; multiple mutant phage strain SG5519; redA and redB mutants
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-
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GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
-
lambda exonuclease is an ATP-independent, but Mg2+-dependent enzyme that binds to dsDNA ends and processively digests the 5'-ended strand to form 5' mononucleotides and a long 3'-ended ssDNA tail
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SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
-
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
degradation also at single-stranded breaks within DNA-duplex
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
degrades double-stranded native DNA
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
-
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
exonucleolytic cleavage in the 5'- to 3'-direction to yield 5'-phosphomononucleotides
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
degradation also at single-stranded breaks within DNA-duplex
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
possess "red" recombination system
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
high processivity
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
no activity on denatured DNA or RNA
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
degrades native DNA 100 times faster than long single-stranded DNA or oligonucleotides
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
shows strong preference for termini bearing 5'-phosphoryl groups
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
no attack at single-stranded breaks within DNA-duplex
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
degrades double-stranded native DNA
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
preference for a 5'-phosphoryl group over a 5'-hydroxyl group
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
lambda exonuclease is unable to initiate DNA digestion at nicks or gaps
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
-
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
exonucleolytic cleavage in the 5'- to 3'-direction to yield 5'-phosphomononucleotides
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
possess "red" recombination system
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
high processivity
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
no activity on denatured DNA or RNA
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
degrades native DNA 100 times faster than long single-stranded DNA or oligonucleotides
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
shows strong preference for termini bearing 5'-phosphoryl groups
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
no attack at single-stranded breaks within DNA-duplex
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
degrades double-stranded native DNA
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
preference for a 5'-phosphoryl group over a 5'-hydroxyl group
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
-
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
-
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
no activity on denatured DNA or RNA
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
degrades double-stranded native DNA
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
-
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
activity depends on lenght of double-stranded DNA
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
high processivity
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
degrades double-stranded native DNA
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
lambda exonuclease selectively digests the phosphorylated undesired strand of double-stranded DNA and produces single-stranded DNA in high yield and purity
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
sequence-dependent rate and pausing of individual lambda exonuclease enzymes during the digestion of a DNA sequence containing 120 CGG repeats. GC-rich repetitive sequences provide a significant barrier to lambda exonuclease activity by increasing the probability of pausing in addition to reducing the average digestion rate
-
-
?
oligonucleotides + H2O
5'-phosphomononucleotides
-
strong preference for relatively short chain oligonucleotides
-
-
-
oligonucleotides + H2O
5'-phosphomononucleotides
-
strong preference for relatively short chain oligonucleotides
-
-
-
single-stranded DNA + H2O
5'-phosphomononucleotides
-
mechanism for stimulation of recombination
-
-
?
single-stranded DNA + H2O
5'-phosphomononucleotides
-
degrades the 5'-terminated strand at a single-stranded branch
-
-
?
single-stranded DNA + H2O
5'-phosphomononucleotides
-
rate of digestion and binding is inversely related to the chain lenght
-
-
?
single-stranded DNA + H2O
5'-phosphomononucleotides
-
digestion not processively
-
-
?
single-stranded DNA + H2O
5'-phosphomononucleotides
-
at single-stranded DNA branches
-
-
?
single-stranded DNA + H2O
5'-phosphomononucleotides
-
mechanism for stimulation of recombination
-
-
?
single-stranded DNA + H2O
5'-phosphomononucleotides
-
degrades the 5'-terminated strand at a single-stranded branch
-
-
?
single-stranded DNA + H2O
5'-phosphomononucleotides
-
rate of digestion and binding is inversely related to the chain lenght
-
-
?
single-stranded DNA + H2O
5'-phosphomononucleotides
-
digestion not processively
-
-
?
single-stranded DNA + H2O
5'-phosphomononucleotides
-
binds to circular or linear single-stranded DNA
-
-
?
single-stranded DNA + H2O
5'-phosphomononucleotides
-
at single-stranded DNA branches
-
-
?
single-stranded DNA + H2O
5'-phosphomononucleotides
-
degrades ssDNA at higher enzyme concentrations
-
-
?
additional information
?
-
-
for enzyme digestion of single DNA molecules, individual lambda-DNA molecules labeled with the fluorescent dye, YOYO-1, are stretched in a laminar flow stream and immobilized on a bare fused-silica prism surface based on hydrophobic and electrostatic interactions. Enzyme digestion is initiated by the influx of lambda-exonuclease enzyme via capillary force, method evaluation, overview. Progression of single-DNA digestion by lambda-exonuclease enzyme based on the decrease in the length of the DNA molecule at a dye:bp ratio of 1:5
-
-
-
additional information
?
-
-
the enzyme unwinds the DNA prior to cleavage, such that two nucleotides of the 5'-ended strand insert into the active site of one subunit of the trimer, while the 3'-ended strand passes through the central channel to emerge out the back of the trimer. Unwinding of the DNA is facilitated by several apolar residues, including Leu78, that wedge into the base pairs at the single/double-strand junction to form favorable hydrophobic interactions. The terminal 5' phosphate of the DNA binds to a positively charged pocket buried at the end of the active site, while the scissile phosphate bridges two active site Mg2+ ions, mechanism of progressivity, structure-activity analysis, overview
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-
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NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
-
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
-
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
-
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
-
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
-
-
-
?
double-stranded DNA + H2O
single-stranded DNA + 5'-phospho-2'-deoxynucleotides
-
-
-
-
?
single-stranded DNA + H2O
5'-phosphomononucleotides
-
at single-stranded DNA branches
-
-
?
single-stranded DNA + H2O
5'-phosphomononucleotides
-
at single-stranded DNA branches
-
-
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Mn2+
Mn2+
-
divalent cation: Mn2+ or Mg2+ required; optimal concentration 1 mM
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
9.2 - 9.5
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7 - 10.2
7.5
9.6
7 - 10.2
-
pH 7.0: 16%, 8.0: 35%, pH 10.0: 35%, 10.2: 8% of maximal activity
7 - 10.2
-
pH 7.0: 16%, 8.0: 35%, pH 10.0: 35%, 10.2: 8% of maximal activity
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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PDB
SCOP
CATH
ORGANISM
UNIPROT
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
24000
28000
28000
-
alpha,beta, 1 * 24000 + 1 * 28000, exonuclease and beta protein as subunits, SDS-PAGE at the presence of urea
28000
-
alpha,beta, 1 * 24000 + 1 * 28000, exonuclease and beta protein as subunits, SDS-PAGE at the presence of urea
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dimer
trimer
dimer
-
alpha,beta, 1 * 24000 + 1 * 28000, exonuclease and beta protein as subunits, SDS-PAGE at the presence of urea
dimer
-
alpha,beta, 1 * 24000 + 1 * 28000, exonuclease and beta protein as subunits, SDS-PAGE at the presence of urea
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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
60
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
repeated freezing and thawing causes loss of activity
stability enhanced by dithiothreitol
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, 40% glycerol, 1mg/ml bovine serum albumin, 6 months, 0% loss of activity
-20°C, in solution, 1 year, 10% loss of activity
0°C, in solution, 2 months, little loss of activity
-20°C, 40% glycerol, 1mg/ml bovine serum albumin, 6 months, 0% loss of activity
-
-20°C, 40% glycerol, 1mg/ml bovine serum albumin, 6 months, 0% loss of activity
-
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
lambda mutant T11 overexpress the enzyme; multiple mutant phage strain SG5519 as source of the enzyme
partial
subfractions upon gradient chromatography: IVa, IVb, phage-lambda induced enzyme; to homogeneity
lambda mutant T11 overexpress the enzyme; multiple mutant phage strain SG5519 as source of the enzyme
-
lambda mutant T11 overexpress the enzyme; multiple mutant phage strain SG5519 as source of the enzyme
-
subfractions upon gradient chromatography: IVa, IVb, phage-lambda induced enzyme; to homogeneity
-
subfractions upon gradient chromatography: IVa, IVb, phage-lambda induced enzyme; to homogeneity
-
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
K49A
-
site-directed mutagenesis, the mutant shows activity similar to the wild-type enzyme
K76A
-
site-directed mutagenesis, the mutant shows activity similar to the wild-type enzyme
L78A
-
site-directed mutagenesis, the mutant shows a significantly diminished level of activity compared to the wild-type enzyme
M53A
-
site-directed mutagenesis, the mutant shows activity similar to the wild-type enzyme
R28A
-
site-directed mutagenesis, mutation of a residue that contact the 5' phosphate of the DNA, inactive mutant
W24A
-
site-directed mutagenesis, mutation of a residue that contact the 5' phosphate of the DNA, almost inactive mutant
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
analysis
synthesis
-
solid-phase digestion of dsDNAs using immobilization of lambda exonuclease onto poly(methylmethacrylate) micropillars populated within a microfluidic device for the on-chip digestion. The efficiency for the catalysis of dsDNA digestion using lamba-exonuclease, including its processivity and reaction rate, are higher when the enzyme is attached to a solid support compared to the free solution digestion. A clipping rate of 1000 nucleotides per s can be obtained for the digestion of lambda-DNA (48.5 kbp) by lambda-exonuclease
additional information
-
preparation of single-stranded DNA is an essential and important step in the combinatorial chemistry technique SELEX (Systematic Evolution of Ligands by EXponential enrichment) for in vitro selection of single-stranded DNA aptamers and numerous other molecular biology procedures, whereby single-stranded DNA generation by lambda exonuclease digestion is superior to other techniques. Important role for complete lambda exonuclease digestion of phosphorylated DNA strand plays the manufacturing of phosphorylated primer
analysis
-
use as reagent restriction mapping and substrate preparation
analysis
-
for studies of genetic recombination; use as reagent for determination of secondary structures at DNA termini; use as reagent restriction mapping and substrate preparation
analysis
-
for studies of genetic recombination; use as reagent for determination of secondary structures at DNA termini; use as reagent restriction mapping and substrate preparation
analysis
ultiplexed single-molecule assay for enzymatic activity on flow-stretched DNA can be applied to lambda exonuclease
analysis
-
a novel method for real-time monitoring of the activity and kinetics of T4 polynucleotide kinase (PNK) by use of a singly fluorophore-labeled DNA-hairpin smart probe (SP) coupled with lambda exonuclease (lambda exo) cleavage.
analysis
-
simple and homogeneous microRNA assay by integration of ligase chain reaction and lambda exonuclease-assisted cationic conjugated polymer biosensing. Ligase chain reaction is utilized for exponential amplification of microRNA, and lambda exonuclease is introduced to degrade excess fluorescein-labeled probes in ligase chain reaction for eliminating background signal. The method is sensitive enough to detect 0.1 fM target microRNA and specific to discriminate one-base difference of microRNAs
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LINKS TO OTHER DATABASES (specific for EC-Number 3.1.11.3)
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