6.5.1.1: DNA ligase (ATP)

This is an abbreviated version!
For detailed information about DNA ligase (ATP), go to the full flat file.

Reaction

Synonyms

adenosine triphosphate-dependent ligase, ADL, APE1094, ApeLig, ATP-dependent DNA ligase, ATP-dependent DNA ligase 1, ATP-dependent DNA ligase I, ATP-dependent ligase, ATP-dependent ligase LigB, ATP-dependent ligase LigC, ATP-dependent ligase LigD, ATP-type DNA repair ligase, AtuLigD1, AtuLigD2, b-ADL, bacterial ATP-dependent DNA ligase, Cdc9, ChVLig, CVLig, Deoxyribonucleate ligase, Deoxyribonucleic acid joinase, Deoxyribonucleic acid ligase, Deoxyribonucleic acid repair enzyme, Deoxyribonucleic acid-joining enzyme, Deoxyribonucleic joinase, Deoxyribonucleic ligase, Deoxyribonucleic repair enzyme, Deoxyribonucleic-joining enzyme, DNA joinase, DNA ligase, DNA ligase 1, DNA ligase 4, DNA ligase D, DNA ligase I, DNA ligase II, DNA ligase III, DNA ligase IIIalpha, DNA ligase IV, DNA ligase IV homolog, DNA ligase IV-XRCC4 complex, DNA ligase IV/XRCC4 complex, DNA ligase IV/XRCC4/XLF complex, DNA ligase V, DNA ligase VI, DNA repair enzyme, DNA repair ligase D, DNA-joining enzyme, DNAligI, Dnl4, drB0100, Hbu DNA ligase, L3BRCT, LdMNPV DNA ligase, Lig, Lig E, Lig I, Lig III, LIG k alpha, Lig K protein, Lig(Tk), LIG1, Lig3, Lig3alpha, Lig4, LIG6, LigA, ligase 1, ligase D, ligase III, ligase III-alpha, LigB, LigC, LigC1, LigD, LigI, LigIII, LigTh1519, ligTK, MJ0171, MSH-1, Mt-Lig, Mth ligase, MtuLigB, MtuLigC, MtuLigD, NHEJ DNA repair ligase, PabDBD, PaeLigD, PBCV-1 DNA ligase, PF1635, PfLigI, Pfu DNA ligase, PfuLig, Polydeoxyribonucleotide synthase (ATP), Polydeoxyribonucleotide synthase [ATP], Polynucleotide ligase, Sealase, ssLig, SSO0189, T4 ATP ligase, T4 DNA ligase, T4 lig, Vaccinia ligase, Vib-Lig, X4L4, XRCC1/DNA ligase III, XRCC4-DNA ligase IV complex

ECTree

     6 Ligases

         6.5 Forming phosphoric-ester bonds

             6.5.1 Ligases that form phosphoric-ester bonds (only sub-subclass identified to date)

                6.5.1.1 DNA ligase (ATP)

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Results	in table
34	Activating Compound
47549	AA Sequence
9	Application
1	CAS Registry Number
86	Cloned(Commentary)
120	Cofactor
23	Crystallization (Commentary)
1953	Disease/ Diagnostics
2	Expression
34	General Information
9	General Stability
19	IC50 Value
177	Inhibitors
8	kcat/KM [mM/s]
1	Ki Value [mM]
77	KM Value [mM]
39	Localization
119	Metals/Ions
71	Molecular Weight [Da]
164	Natural Substrates/ Products (Substrates)
2	Organic Solvent Stability
348	Organism
66	PDB ID
37	pH Optimum
11	pH Range
1	pH Stability
2	pI Value
1	Posttranslational Modification
141	Protein Variants
105	Purification (Commentary)
9	Reaction
1	Reaction Type
340	Reference
111	Source Tissue
8	Specific Activity [micromol/min/mg]
8	Storage Stability
445	Substrates and Products (Substrate)
72	Subunits
395	Synonyms
1	Systematic Name
30	Temperature Optimum [°C]
10	Temperature Range [°C]
25	Temperature Stability [°C]
30	Turnover Number [1/s]

Activating Compound

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Activating Compound on EC 6.5.1.1 - DNA ligase (ATP)

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ACTIVATING COMPOUND

ORGANISM

UNIPROT

COMMENTARY

LITERATURE

IMAGE

apurine/apyrimidinic endonuclease I

Homo sapiens

-

stimulation of DNA ligase activity, inhibition if the DNA ligase I substrate has a tetrahydrofuran residue on the 5'-downstream primer of a nick, simulating a reduced abasic site

652322

-

bovine serum albumin

Mammalia

-

stimulates

1906

-

dithiothreitol

2 entries

DRB0098 protein

Deinococcus radiodurans

-

DNA ligase activity of LigB is severalfold stimulated by PprA in the presence of the recombinant DRB0098 protein

714069

-

Hexamine cobalt chloride

Tequatrovirus T4

-

maximal stimulation at 0.001-0.0015 mM, blunt end ligation is stimulated 50fold, but cohesive end ligation only 5fold

1910

phosphate

Mammalia

-

DNA ligase I is a phosphoprotein, dephosphorylation causes drastic reduction in enzyme activity

1906

polyamines

Bos taurus

-

polyamines activate at suboptimal concentrations of Mg2+

1920

-

Polyethylene glycol

2 entries

polyvinyl alcohol

Drosophila melanogaster

-

required for optimal activity of DNA ligase I but not for DNA ligase II activity

1965

PprA protein

Deinococcus radiodurans

-

DNA ligase activity of LigB is severalfold stimulated by PprA in the presence of the recombinant DRB0098 protein

714069

-

proliferating cell nuclear antigen

4 entries

-

Reducing agent

4 entries

-

replication protein

Homo sapiens

-

-

652322

-

replication protein A

Homo sapiens

-

approx. 15fold stimulation of DNA ligase I

652248

-

spermidine

Bos taurus

-

5 mM, increases the Km for nicked DNA, increases reaction velocity

1929

spermine

Bos taurus

-

0.5 mM, increases the Km for nicked DNA, increases reaction velocity

1929

T4RNA ligase

Tequatrovirus T4

-

stimulates T4 DNA ligase activity

1910

-

XLF-Cernunnos

Homo sapiens

-

a component of the DNA ligase IV-XRCC4 complex, which functions during DNA non-homologous end joining and stimulates ligase IV re-adenylation following ligation

694470

-

XRCC1

Mammalia

-

DNA ligase III-alpha forms a complex with the DNA single-strand break repair protein XRCC1

1907

-

XRCC4

Homo sapiens

-

stimulates DNA ligase activity primarily through direct structure interaction with DNA ligase

1944

-

additional information

4 entries

-

dithiothreitol

Drosophila melanogaster

-

required for optimal activity of DNA ligase I, but not for DNA ligase II activity

1965

dithiothreitol

Homo sapiens

-

required for optimal activity

1922

Polyethylene glycol

Tequatrovirus T4

-

polyethylene glycol 8000, maximal stimulation at 15%

1910

Polyethylene glycol

Tequatrovirus T4

-

polyethylene glycol 6000, 15%, stimulates, when NaCl and KCl are both absent. With 10% polyethylene glycol 6000, both cohesive end ligation and blunt end ligation are increased at high concentrations of salt, 150-200 mM NaCl, or 200-250 mM KCl. With 10% polyethylene glycol 6000, intermolecular and intramolecular ligation occurs at low salt concentrations, 0.1 mM NaCl or 0-150 mM KCl. Only linear oligomers are formed by intermolecular ligation at the high concentrations

1916

proliferating cell nuclear antigen

Homo sapiens

-

-

652322

-

proliferating cell nuclear antigen

Homo sapiens

-

5fold activation, proliferating cell nuclear antigen improves binding of DNA ligase I to ligation site and is responsible for the stable association of DNA ligase I to nicked duplex DNA

652140

-

proliferating cell nuclear antigen

Pyrococcus furiosus

P56709

stimulatory effect of Pyrococcus furiosus proliferating cell nuclear antigen (PCNA) on the enzyme activity of Pyrococcus furiosus DNA ligase is observed not at low ionic strength, but at a high salt concentration, at which a DNA ligase alone cannot bind to a nicked DNA substrate. Identification of the amino acid residues that are critical for PCNA binding in a loop structure located in the N-terminal DNA-binding domain of Ppyrococcus furiosus DNA ligase. The pentapeptide motif QKSFF is involved in the PCNA-interacting motifs, in which Gln and the first Phe are especially important for stable binding with PCNA

722648

-

proliferating cell nuclear antigen

Saccharolobus solfataricus

Q980T8

-

747025

-

Reducing agent

Escherichia phage T7

-

reducing agents, e.g. 2-mercaptoethanol or dithiothreitol required

1909, 1910

-

Reducing agent

eukaryota

-

reducing agents, e.g. 2-mercaptoethanol or dithiothreitol required

1909

-

Reducing agent

Mammalia

-

reducing agents, e.g. 2-mercaptoethanol or dithiothreitol required

1909, 1910

-

Reducing agent

Tequatrovirus T4

-

reducing agents, e.g. 2-mercaptoethanol or dithiothreitol required

1909, 1910

-

additional information

Homo sapiens

-

LigI activity is strongly linked to proliferating cell nuclear antigen, the interaction between both factors is essential for the recruitment of LigI to replication foci and sites of DNA damage, replication efficiency is reduced on CTG/CAG templates with a defective LigI

709055

-

additional information

Mammalia

-

human fibroblast line GM1492, but not several related fibroblast lines, expresses substantial amounts of a heat-stable protease-sensitive factor, which stimulates calf thymus DNA ligase I

1906

-

additional information

Saccharolobus solfataricus

Q980T8

the enzyme interacts with the proliferating cell nuclear antigen heterotrimer

725969

-

additional information

Saccharolobus solfataricus

-

the enzyme interacts with the proliferating cell nuclear antigen heterotrimer

725969

-