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HAMAP rule MF_00407

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General rule information [?]

Accession MF_00407
Dates 1-JUN-2001 (Created)
1-JUN-2023 (Last updated, Version 33)
Name DNA_ligase
Scope(s) Bacteria
Archaea
Template(s) P56709 (DNLI_PYRFU); Q9HHC4 (DNLI_THEKO); Q980T8 (DNLI_SACS2); Q9P9K9 (DNLI_SACSH); A2BJX6 (DNLI_HYPBU); [ Recover all ]
Triggered by HAMAP; MF_00407 (Get profile general information and statistics)

Propagated annotation [?]

Identifier, protein and gene names [?]

Identifier DNLI
case <OC:Archaea> and not <OC:Thermococcus>
Protein name RecName: Full=DNA ligase;
                 EC=6.5.1.1;
AltName: Full=Polydeoxyribonucleotide synthase [ATP];
else case <OC:Thermococcus>
Protein name RecName: Full=DNA ligase;
                 EC=6.5.1.6;
AltName: Full=Polydeoxyribonucleotide synthase [ATP/NAD(+)];
else case <OC:Bacteria>
Protein name RecName: Full=Probable DNA ligase;
                 EC=6.5.1.1;
AltName: Full=Polydeoxyribonucleotide synthase [ATP];
end case
Gene name Name=lig;

Comments [?]

FUNCTIONDNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair.
case <OC:Archaea> and not <OC:Thermococcus>
CATALYTIC ACTIVITY Reaction=ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho- (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + diphosphate.; EC=6.5.1.1;
else case <OC:Thermococcus>
CATALYTIC ACTIVITY Reaction=ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho- (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + diphosphate.; EC=6.5.1.6;
CATALYTIC ACTIVITY Reaction=NAD(+) + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho- (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + beta- nicotinamide D-nucleotide.; EC=6.5.1.6;
else case <OC:Bacteria>
CATALYTIC ACTIVITY Reaction=ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho- (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP + diphosphate.; EC=6.5.1.1;
end case
COFACTOR Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
SIMILARITYBelongs to the ATP-dependent DNA ligase family.

Keywords [?]

DNA damage
DNA repair
DNA replication
DNA recombination
Cell cycle
Cell division
Ligase
ATP-binding
Magnesium
Metal-binding
case <OC:Thermococcus>
NAD
end case
Nucleotide-binding

Gene Ontology [?]

GO:0005524; Molecular function:ATP binding
GO:0003910; Molecular function:DNA ligase (ATP) activity
GO:0006310; Biological process:DNA recombination
GO:0006281; Biological process:DNA repair
GO:0006260; Biological process:DNA replication

Cross-references [?]

Pfam PF04679; DNA_ligase_A_C; 1;
Pfam PF01068; DNA_ligase_A_M; 1;
Pfam PF04675; DNA_ligase_A_N; 1;
NCBIfam TIGR00574; Dnl1; 1;
PROSITE PS00697; DNA_LIGASE_A1; 1;
PROSITE PS00333; DNA_LIGASE_A2; 1;
PROSITE PS50160; DNA_LIGASE_A3; 1;

Features [?]

From: DNLI_PYRFU (P56709)
Key From To Description Tag Condition FTGroup
ACT_SITE 249 249 /note="N6-AMP-lysine intermediate" K
BINDING 247 247 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"		 [DE]
BINDING 254 254 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"		 R
BINDING 269 269 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"		 R
BINDING 299 299 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"		 E
BINDING 339 339 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"		 F
BINDING 414 414 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"		 R
BINDING 420 420 /ligand="ATP"
/ligand_id="ChEBI:CHEBI:30616"		 K

Additional information [?]

Size range 503-618 amino acids
Related rules None
Fusion Nter: <Unknown> Cter: None
Comments Shorter N-terminus in the first copy of lig in METBF. Some archaea use additional nucleotide cofactors (such as NAD(+), ADP or GTP) next to ATP.



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