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Information on EC 6.5.1.1 - DNA ligase (ATP) and Organism(s) Entamoeba histolytica and UniProt Accession C4M5H3
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6.5.1.1 DNA ligase (ATP)IUBMB Comments
The enzyme catalyses the ligation of DNA strands with 3'-hydroxyl and 5'-phosphate termini, forming a phosphodiester and sealing certain types of single-strand breaks in duplex DNA. Catalysis occurs by a three-step mechanism, starting with the activation of the enzyme by ATP, forming a phosphoramide bond between adenylate and a lysine residue. The adenylate group is then transferred to the 5'-phosphate terminus of the substrate, forming the capped structure 5'-(5'-diphosphoadenosine)-[DNA]. Finally, the enzyme catalyses a nucleophilic attack of the 3'-OH terminus on the capped terminus, which results in formation of the phosphodiester bond and release of the adenylate. RNA can also act as substrate, to some extent. cf. EC 6.5.1.2, DNA ligase (NAD+), EC 6.5.1.6, DNA ligase (ATP or NAD+), and EC 6.5.1.7, DNA ligase (ATP, ADP or GTP).
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Word Map
- 6.5.1.1
- strand
- endonuclease
- nick
-
single-stranded
- ligases
- glycosylase
-
end-joining
-
nonhomologous
- duplex
- mismatch
- polymerases
-
phosphodiester
- dna-pkcs
-
polyadp-ribose
-
topoisomerase
- parp
- 8-oxoguanine
- temozolomide
-
dna-dependent
-
o6-methylguanine-dna
-
rejoin
- uracil
-
abasic
-
okazaki
-
blunt-ended
-
artemis
- fen1
- o6-methylguanine
- primase
-
o6-alkylguanine-dna
-
cross-complementing
-
tyrosyl-dna
-
overhang
-
apurinic
-
alkyltransferase
-
5'-phosphorylated
-
photolyase
-
uracil-dna
-
8-oxog
- mre11
-
mispaired
-
excises
- analysis
-
formamidopyrimidine-dna
- molecular biology
- 7,8-dihydro-8-oxoguanine
- o6-benzylguanine
- formamidopyrimidine
-
o6-alkylguanine
-
base-excision
- synthesis
-
klenow
- smurf1
The taxonomic range for the selected organisms is: Entamoeba histolytica
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Reaction Schemes
hide(Overall reactions are displayed. Show all >>)
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=
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5'-phospho-(deoxyribonucleotide)m
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Synonyms
dna ligase, dna repair enzyme, dna ligase i, t4 dna ligase, dna ligase iv, dna ligase iii, ligase 1, dna ligase ii, polynucleotide ligase, dna ligase 1, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
Deoxyribonucleate ligase
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-
-
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Deoxyribonucleic acid joinase
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-
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Deoxyribonucleic acid ligase
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-
-
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Deoxyribonucleic acid repair enzyme
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-
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Deoxyribonucleic acid-joining enzyme
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-
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Deoxyribonucleic joinase
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-
-
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Deoxyribonucleic ligase
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-
-
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Deoxyribonucleic repair enzyme
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-
-
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Deoxyribonucleic-joining enzyme
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-
-
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DNA joinase
-
-
-
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DNA ligase
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-
-
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DNA ligase I
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-
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DNA ligase II
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-
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DNA ligase III
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-
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DNA ligase IV homolog
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-
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DNA repair enzyme
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-
-
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DNA-joining enzyme
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-
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Lig(Tk)
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-
-
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Pfu DNA ligase
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-
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Polydeoxyribonucleotide synthase (ATP)
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-
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Polydeoxyribonucleotide synthase [ATP]
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-
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Polynucleotide ligase
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Sealase
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SYSTEMATIC NAME
IUBMB Comments
poly(deoxyribonucleotide)-3'-hydroxyl:5'-phospho-poly(deoxyribonucleotide) ligase (ATP)
The enzyme catalyses the ligation of DNA strands with 3'-hydroxyl and 5'-phosphate termini, forming a phosphodiester and sealing certain types of single-strand breaks in duplex DNA. Catalysis occurs by a three-step mechanism, starting with the activation of the enzyme by ATP, forming a phosphoramide bond between adenylate and a lysine residue. The adenylate group is then transferred to the 5'-phosphate terminus of the substrate, forming the capped structure 5'-(5'-diphosphoadenosine)-[DNA]. Finally, the enzyme catalyses a nucleophilic attack of the 3'-OH terminus on the capped terminus, which results in formation of the phosphodiester bond and release of the adenylate. RNA can also act as substrate, to some extent. cf. EC 6.5.1.2, DNA ligase (NAD+), EC 6.5.1.6, DNA ligase (ATP or NAD+), and EC 6.5.1.7, DNA ligase (ATP, ADP or GTP).
CAS REGISTRY NUMBER
COMMENTARY
9015-85-4
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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
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
AMP + diphosphate + (deoxyribonucleotide)m+n
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-
-
?
additional information
?
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DNAligI performs the three conserved steps of a DNA ligation reaction: adenylation, binding to a 5'-phosphorylated nicked DNA substrate and sealing of the nick. DNAligI is also able to ligate a RNA strand upstream of a nucleic acid nick, but not in the downstream or the template position
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-
?
additional information
?
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DNAligI performs the three conserved steps of a DNA ligation reaction: adenylation, binding to a 5'-phosphorylated nicked DNA substrate and sealing of the nick. DNAligI is also able to ligate a RNA strand upstream of a nucleic acid nick, but not in the downstream or the template position
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-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
DNAligI is not active using NAD+, UTP, CTP, GTP, dATP, and dGTP as cofactors
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additional information
-
DNAligI is not active using NAD+, UTP, CTP, GTP, dATP, and dGTP as cofactors
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
DNAligI uses Mn2+ or Mg2+ as metal cofactors, optimal ligation activity at 4 mM of Mg2+
Mn2+
DNAligI uses Mn2+ or Mg2+ as metal cofactors, optimal ligation activity at 1 mM of Mn2+
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.000064
ATP
in 50 mM Tris pH 7.5, 100 mM NaCl, 10 mM dithiothreitol, at 21°C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.04
ATP
in 50 mM Tris pH 7.5, 100 mM NaCl, 10 mM dithiothreitol, at 21°C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
625
ATP
in 50 mM Tris pH 7.5, 100 mM NaCl, 10 mM dithiothreitol, at 21°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6.5 - 8.5
DNAligI activity gradually increases from pH 6.5 to 8.0 and displays a sharp decline at pH 8.5
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
a population of the DNAligI protein is translocated from the cytoplasm into the nuclei
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
DNAligI is involved in sealing DNA nicks during lagging strand synthesis and may have a role in base excision repair in Entamoeba histolytica
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). C4M5H3_ENTHI
685
0
78164
TrEMBL
Mitochondrion (Reliability: 5)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
HiTrap column chromatography and phosphocellulose column chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Cardona-Felix, C.S.; Pastor-Palacios, G.; Cardenas, H.; Azuara-Liceaga, E.; Brieba, L.G.
Biochemical characterization of the DNA ligase I from Entamoeba histolytica
Mol. Biochem. Parasitol.
174
26-35
2010
Entamoeba histolytica (C4M5H3), Entamoeba histolytica, Entamoeba histolytica HM1:IMSS (C4M5H3)
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