Information on EC 3.1.11.3 - exodeoxyribonuclease (lambda-induced)

strong preference for relatively short chain oligonucleotides

133978, 133980

oligonucleotides + H2O

5'-phosphomononucleotides

low rate

oligonucleotides + H2O

5'-phosphomononucleotides

strong preference for relatively short chain oligonucleotides

133978, 133980

oligonucleotides + H2O

5'-phosphomononucleotides

low rate

single-stranded DNA + H2O

5'-phosphomononucleotides

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

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

show all columns Go to Natural Substrate Search

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NATURAL SUBSTRATE

NATURAL PRODUCT

REACTION DIAGRAM

ORGANISM

UNIPROT

COMMENTARY
(Substrate)

LITERATURE
(Substrate)

COMMENTARY
(Product)

LITERATURE
(Product)

REVERSIBILITY
r=reversible
ir=irreversible
?=not specified

double-stranded DNA + H2O

single-stranded DNA + 5'-phospho-2'-deoxynucleotides

6 entries

single-stranded DNA + H2O

5'-phosphomononucleotides

double-stranded DNA + H2O

single-stranded DNA + 5'-phospho-2'-deoxynucleotides

double-stranded DNA + H2O

single-stranded DNA + 5'-phospho-2'-deoxynucleotides

133978, 133980, 133981, 133983, 133984, 133985, 133986, 133987, 133988, 133989

double-stranded DNA + H2O

single-stranded DNA + 5'-phospho-2'-deoxynucleotides

Escherichia virus Lambda phage 80

133978, 133980, 133983, 133984, 133985, 133986, 133987, 133988, 133989

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

single-stranded DNA + H2O

5'-phosphomononucleotides

at single-stranded DNA branches

single-stranded DNA + H2O

5'-phosphomononucleotides

single-stranded DNA + H2O

5'-phosphomononucleotides

at single-stranded DNA branches

show all columns Go to Metals and Ions Search

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METALS and IONS

ORGANISM

UNIPROT

COMMENTARY

LITERATURE

Mg2+

9 entries

Mn2+

5 entries

Mg2+

optimal concentration 5 mM; required

Mg2+

optimal concentration 5 mM; required

Mg2+

required

Mg2+

required

Mg2+

activates

Mg2+

dependent on

Mg2+

required

Mg2+

required

Mg2+

synthetic construct

initiates DNA digestion

708359

Mn2+

divalent cation: Mn2+ or Mg2+ required; optimal concentration 1 mM

Mn2+

divalent cation: Mn2+ or Mg2+ required; optimal concentration 1 mM

Mn2+

divalent cation: Mn2+ or Mg2+ required

Mn2+

divalent cation: Mn2+ or Mg2+ required

Mn2+

divalent cation: Mn2+ or Mg2+ required

show all columns Go to Inhibitor Search

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INHIBITOR

ORGANISM

UNIPROT

COMMENTARY

LITERATURE

IMAGE

high pressure

KCl

NaCl

p-chloromercuribenzoate

high pressure

hydrostatic pressure controles activity

high pressure

hydrostatic pressure controles activity

KCl

31% inhibition at 50 mM

KCl

31% inhibition at 50 mM

KCl

NaCl

82% inhibition at 50 mM

NaCl

82% inhibition at 50 mM

NaCl

NaCl

inhibition at concentrations over 70 mM

p-chloromercuribenzoate

p-chloromercuribenzoate

p-chloromercuribenzoate

show all columns Go to Activating Compound Search

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ACTIVATING COMPOUND

ORGANISM

UNIPROT

COMMENTARY

LITERATURE

IMAGE

2-mercaptoethanol

dithiothreitol

KCl

NaCl

82% stimulation up to 70 mM

dithiothreitol

required

dithiothreitol

required

KCl

show all columns Go to KM Value Search

stimulates at 20 mM

KCl

stimulates at 20 mM

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KM VALUE [mM]

SUBSTRATE

ORGANISM

UNIPROT

COMMENTARY

LITERATURE

IMAGE

0.0000018

DNA

0.0000018

DNA

5'-OH blunt end double-stranded DNA

0.0000018

DNA

5'-OH blunt end double-stranded DNA

show all columns Go to Turnover Number Search

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TURNOVER NUMBER [1/s]

SUBSTRATE

ORGANISM

UNIPROT

COMMENTARY

LITERATURE

IMAGE

6 - 11.7

Double-stranded DNA

Double-stranded DNA

at 20°C and pH 7.5

Double-stranded DNA

at 20°C and pH 7.5

11.7

Double-stranded DNA

at 37°C and pH 7.5

11.7

Double-stranded DNA

at 37°C and pH 7.5

show all columns Go to pH Optimum Search

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pH OPTIMUM

ORGANISM

UNIPROT

COMMENTARY

LITERATURE

7.7

8 - 8.5

9.2 - 9.5

9.4

assay at

9.2 - 9.5

9.2 - 9.5

show all columns Go to pH Range Search

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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

7.5

no activity at DNA nicks

7.5

no activity at DNA nicks

9.6

no activity at DNA nicks

9.6

no activity at DNA nicks

show all columns Go to Temperature Optimum Search

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TEMPERATURE OPTIMUM

ORGANISM

UNIPROT

COMMENTARY

LITERATURE

assay at

show all columns Go to Organism Search

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ORGANISM

COMMENTARY

LITERATURE

UNIPROT

SEQUENCE DB

SOURCE

brenda

Escherichia virus Lambda phage 80

5 entries

phage 80

brenda

brenda

yeast

brenda

brenda

brenda

Escherichia coli infected with phage lambda only

133972, 133978, 133979, 133980, 133981, 133983, 133984, 133985, 133986, 133987, 133988, 133989, 133993

brenda

Escherichia coli infected with phage lambda only; recB gene

brenda

133972, 133978, 133979, 133983, 133984, 133986, 133987, 133989, 133992, 133993, 713754, 716778, 728851, 728953

brenda

682074

UniProt

brenda

defective lambda mutant T11; multiple mutant phage strain SG5519; redA and redB mutants

brenda

mutants with increased thermostability; redA and redB mutants

133985

brenda

phage 80

brenda

show all columns Go to Source Tissue Search

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SOURCE TISSUE

ORGANISM

UNIPROT

COMMENTARY

LITERATURE

SOURCE

commercial preparation

695543, 695561

brenda

lung

brenda

show all columns Go to Localization Search

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LOCALIZATION

ORGANISM

UNIPROT

COMMENTARY

GeneOntology No.

LITERATURE

SOURCE

nucleus

5634

brenda

show all columns Go to General Information Search

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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

Go to AA Sequence and Transmembrane Helices Search

Show AA Sequence and Transmembrane Helices (109 entries)
Please use the AA Sequence and Transmembrane Helices Search for a specific query.

Go to PDB and Structure Links Search

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PDB

SCOP

CATH

UNIPROT

ORGANISM

5 entries

Escherichia phage lambda

1avq, download, 3D-view

SCOPe (1avq)

CATH (1avq)

Escherichia phage lambda

3slp, download, 3D-view

SCOPe (3slp)

CATH (3slp)

Escherichia phage lambda

3sm4, download, 3D-view

SCOPe (3sm4)

CATH (3sm4)

Escherichia phage lambda

4wuz, download, 3D-view

SCOPe (4wuz)

CATH (4wuz)

Escherichia phage lambda

6m9k, download, 3D-view

SCOPe (6m9k)

CATH (6m9k)

Escherichia phage lambda

show all columns Go to Molecular Weight Search

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MOLECULAR WEIGHT

ORGANISM

UNIPROT

COMMENTARY

LITERATURE

24000

28000

42000

sedimentation, gel filtration

70000

gel fitration, SDS-PAGE

24000

gene sequence

24000

gene sequence

24000

gel fitration, SDS-PAGE

24000

gel fitration, SDS-PAGE

28000

alpha,beta, 1 * 24000 + 1 * 28000, exonuclease and beta protein as subunits, SDS-PAGE at the presence of urea

28000

show all columns Go to Subunit Search

alpha,beta, 1 * 24000 + 1 * 28000, exonuclease and beta protein as subunits, SDS-PAGE at the presence of urea

28000

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SUBUNIT

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

trimer

crystal structure

trimer

crystal structure

Go to Crystallization Search

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CRYSTALLIZATION/commentary

ORGANISM

UNIPROT

LITERATURE

by ammonium sulfate precepitation

by ammonium sulfate precepitation

show all columns Go to Protein Variants Search

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PROTEIN VARIANTS

ORGANISM

UNIPROT

COMMENTARY

LITERATURE

D119A

site-directed mutagenesis, inactive mutant

E85A

site-directed mutagenesis, almost inactive mutant

K131A

site-directed mutagenesis, inactive mutant

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

R137A

site-directed mutagenesis, inactive mutant

R28A

site-directed mutagenesis, mutation of a residue that contact the 5' phosphate of the DNA, inactive mutant

R45A

site-directed mutagenesis, inactive mutant

W24A

site-directed mutagenesis, mutation of a residue that contact the 5' phosphate of the DNA, almost inactive mutant

show all columns Go to Temperature Stability Search

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TEMPERATURE STABILITY

ORGANISM

UNIPROT

COMMENTARY

LITERATURE

complete inactivation after 5 min without substrate

complete inactivation after 5 min without substrate

Go to General Stability Search

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GENERAL STABILITY

ORGANISM

UNIPROT

LITERATURE

repeated freezing and thawing causes loss of activity

stability enhanced by dithiothreitol

repeated freezing and thawing causes loss of activity

repeated freezing and thawing causes loss of activity

stability enhanced by dithiothreitol

stability enhanced by dithiothreitol

Go to Storage Stability Search

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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

-20°C, in solution, 1 year, 10% loss of activity

-20°C, in solution, 1 year, 10% loss of activity

0°C, in solution, 2 months, little loss of activity

0°C, in solution, 2 months, little loss of activity

Go to Purification Search

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PURIFICATION/commentary

ORGANISM

UNIPROT

LITERATURE

crosses of phage 80 and lambda

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

133985, 133987, 133988, 133989

133985, 133987, 133989

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

partial

partial

partial

partial

subfractions upon gradient chromatography: IVa, IVb, phage-lambda induced enzyme; to homogeneity

subfractions upon gradient chromatography: IVa, IVb, phage-lambda induced enzyme; to homogeneity

show all columns Go to Application Search

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APPLICATION

ORGANISM

UNIPROT

COMMENTARY

LITERATURE

analysis

10 entries

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

728953

additional information

synthetic construct

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

710025

analysis

use as reagent restriction mapping and substrate preparation

133972

analysis

use as reagent restriction mapping and substrate preparation

133972

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

for studies of genetic recombination

133985, 133988

analysis

for studies of genetic recombination

133985, 133988

analysis

ultiplexed single-molecule assay for enzymatic activity on flow-stretched DNA can be applied to lambda exonuclease

682074

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.

695561

analysis

Escherichia virus Lambda phage 80

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

728851

analysis

for studies of genetic recombination

top print hide References Search

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REF.

AUTHORS

TITLE

JOURNAL

VOL.

PAGES

YEAR

ORGANISM (UNIPROT)

PUBMED ID

SOURCE

133972

Pierce, J.R.; Nazimiec, M.; Tang, M.s.

Comparison of sequence preference of tomaymycin- and anthramycin-DNA bonding by exonuclease III and lambda exonuclease digestion and UvrABC nuclease incision analysis

Biochemistry

7069-7078

1993

Escherichia coli, Escherichia virus Lambda

8343501

brenda

133978

Lehman, I.R.

Bacterial deoxyribonucleases

The Enzymes, 3rd Ed. (Boyer, P. D. , ed. )

251-270

1971

Escherichia coli, Escherichia virus Lambda

brenda

Mitsis, P.G.; Kwagh, J.G.

Characterization of the interaction of lambda exonuclease with the ends of DNA

Nucleic Acids Res.

3057-3063

1999

Escherichia coli, Escherichia virus Lambda

10454600

brenda

Little, J.W.

Lambda exonuclease

Gene Amplif. Anal.

135-145

1981

Escherichia coli, Escherichia virus Lambda

6242844

brenda

Kerr, C.; Sadowski, P.D.

Gene 6 exonuclease of bacteriophage T7. I. Purification and properties of the enzyme

J. Biol. Chem.

247

305-310

1972

Enterobacteria phage T7, Escherichia coli

4336366

brenda

Lindahl, T.

An exonuclease specific for double-stranded DNA: deoxyribonuclease from rabbit tissues

Methods Enzymol.

148-153

1971

Oryctolagus cuniculus

brenda

Sriprakash, K.S.; Lundh, N.; Huh, M.M.O.; Radding, C.M.

The specificity of lambda exonuclease. Interactions with single-atranded DNA

J. Biol. Chem.

250

5438-5445

1975

Escherichia coli, Escherichia virus Lambda

1141237

brenda

Cassuto, E.; Radding, C.M.

Mechanism for the action of lambda exonuclease in genetic recombination

Nature New Biol.

229

13-16

1971

Escherichia coli, Escherichia virus Lambda

5276049

brenda

133985

Radding, C.M.

The role of exonuclease and beta protein of bacteriophage lambda in genetic recombination. I. Effects of red mutants on protein structure

J. Mol. Biol.

491-499

1970

Escherichia coli, Escherichia virus Lambda

4992641

brenda

Little, J.W.; Lehman, I.R.; Kaiser, A.D.

An exonuclease induced by bacteriophage lambda. I. Preparation of the crystalline enzyme

J. Biol. Chem.

242

672-678

1967

Escherichia coli, Escherichia virus Lambda

6017736

brenda

133987

Little, J.W.

An exonuclease induced by bacteriophage lambda. II. Nature of the enzymatic reaction

J. Biol. Chem.

242

679-686

1967

Escherichia coli, Escherichia virus Lambda

6017737

brenda

Radding, C.M.; Szpirer, J.; Thomas, R.

The structural gene for lambda exonuclease

Proc. Natl. Acad. Sci. USA

277-283

1967

Escherichia coli, Escherichia virus Lambda, Escherichia virus Lambda phage 80

16591465

brenda

Carter, D.M.; Radding, C.M.

The role of exonuclease and beta protein of phage lambda in genetic recombination. II. Substrate specificity and the mode of action of lambda exonuclease

J. Biol. Chem.

246

2502-2512

1971

Escherichia coli, Escherichia virus Lambda

4928646

brenda

Dolberg, M.; Baur, C.P.; Knippers, R.

Purification and characterization of a novel 5' exodeoxyribonuclease from the yeast Saccharomyces cerevisiae

Eur. J. Biochem.

198

783-787

1991

Saccharomyces cerevisiae

2050153

brenda

Rudd, E.A.

Reversible inhibition of lambda exonuclease with high pressure

Biochem. Biophys. Res. Commun.

230

140-142

1997

Escherichia coli, Escherichia virus Lambda

9020031

brenda