HAMAP rule MF_00407
General rule information
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| PURL | https://purl.expasy.org/hamap/rule/MF_00407 |
| Accession | MF_00407 |
| Dates | 28-FEB-2005 (Created)
01-JUN-2023 (Last updated, Version 25) |
| Name | DNA_ligase |
| Scope(s) |
Bacteria Archaea |
| Template(s) | P56709; Q9HHC4; Q980T8; Q9P9K9; A2BJX6; [ Recover all ] |
| Triggered by |
HAMAP; MF_00407 (Get profile general information and statistics) |
Propagated annotation
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Identifier, protein and gene names
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| 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
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| FUNCTION | DNA 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; |
| SIMILARITY | Belongs to the ATP-dependent DNA ligase family. |
Keywords
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| 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
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| 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
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| 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
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| 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
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| 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. |