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Lig3 ligase III, DNA, ATP-dependent [ Mus musculus (house mouse) ]

Gene ID: 16882, updated on 3-Apr-2024

Summary

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Official Symbol
Lig3provided by MGI
Official Full Name
ligase III, DNA, ATP-dependentprovided by MGI
Primary source
MGI:MGI:109152
See related
Ensembl:ENSMUSG00000020697 AllianceGenome:MGI:109152
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as
D11Wsu78e
Summary
Predicted to enable DNA ligase (ATP) activity. Involved in double-strand break repair via alternative nonhomologous end joining and mitochondrion organization. Acts upstream of or within double-strand break repair via nonhomologous end joining; mitochondrial DNA repair; and negative regulation of DNA recombination. Located in synaptonemal complex. Is expressed in several structures, including early conceptus; gonad; hemolymphoid system gland; liver; and lung. Human ortholog(s) of this gene implicated in pancreatic cancer. Orthologous to human LIG3 (DNA ligase 3). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis adult (RPKM 26.9), whole brain E14.5 (RPKM 12.7) and 27 other tissues See more
Orthologs
human all
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Genomic context

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Location:
11 C; 11 50.23 cM
Exon count:
22
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (82671977..82695100)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (82781109..82804274)

Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene STARR-positive B cell enhancer ABC_E7027 Neighboring gene zinc finger protein 830 Neighboring gene predicted gene 11423 Neighboring gene ring finger and FYVE like domain containing protein Neighboring gene STARR-seq mESC enhancer starr_30179 Neighboring gene RAD51 paralog D Neighboring gene STARR-positive B cell enhancer ABC_E8433 Neighboring gene fibronectin type III domain containing 8

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Exploiting DNA Ligase III addiction of multiple myeloma by flavonoid Rhamnetin. Caracciolo D, et al. J Transl Med, 2022 Oct 22. PMID 36273153, Free PMC Article
  2. Mitochondrial DNA ligase is dispensable for the viability of cultured cells but essential for mtDNA maintenance. Shokolenko IN, et al. J Biol Chem, 2013 Sep 13. PMID 23884459, Free PMC Article
  3. Time-dependent predominance of nonhomologous DNA end-joining pathways during embryonic development in mice. Chiruvella KK, et al. J Mol Biol, 2012 Mar 30. PMID 22306462
  4. Early embryonic lethality due to targeted inactivation of DNA ligase III. Puebla-Osorio N, et al. Mol Cell Biol, 2006 May. PMID 16648486, Free PMC Article
  5. Loss of nuclear DNA ligase III reverts PARP inhibitor resistance in BRCA1/53BP1 double-deficient cells by exposing ssDNA gaps. Paes Dias M, et al. Mol Cell, 2021 Nov 18. PMID 34555355, Free PMC Article

See all (54) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Exploiting DNA Ligase III addiction of multiple myeloma by flavonoid Rhamnetin.
    Title: Exploiting DNA Ligase III addiction of multiple myeloma by flavonoid Rhamnetin.
  2. Loss of nuclear DNA ligase III reverts PARP inhibitor resistance in BRCA1/53BP1 double-deficient cells by exposing ssDNA gaps.
    Title: Loss of nuclear DNA ligase III reverts PARP inhibitor resistance in BRCA1/53BP1 double-deficient cells by exposing ssDNA gaps.
  3. Telomere-internal double-strand breaks (DSBs) are also repaired by a PARP1- and Ligase3-dependent reaction, suggesting alternative non-homologous end-joining (alt-NHEJ), which relies on microhomology at DSBs.
    Title: Telomere-Internal Double-Strand Breaks Are Repaired by Homologous Recombination and PARP1/Lig3-Dependent End-Joining.
  4. Results show that overexpression of DNA ligase III in mitochondria improves mitochondrial base excision repair and enhances cell survival after oxidative stress.
    Title: Overexpression of DNA ligase III in mitochondria protects cells against oxidative stress and improves mitochondrial DNA base excision repair.
  5. data confirm previous work showing that Lig3 is required to maintain mtDNA integrity and function, and highlight a new function of ATM in regulating DNA Lig3 stability and consequently mtDNA repair
    Title: Intrinsic mitochondrial DNA repair defects in Ataxia Telangiectasia.
  6. Lig3 has an essential role in mtDNA maintenance but is dispensable for the viability of cultured cells
    Title: Mitochondrial DNA ligase is dispensable for the viability of cultured cells but essential for mtDNA maintenance.
  7. results establish a role for Lig3 in mitochondria, but distinguish it from its interacting protein Xrcc1
    Title: Crucial role for DNA ligase III in mitochondria but not in Xrcc1-dependent repair.
  8. data reveal that the critical biological role of Lig3 is to maintain mtDNA integrity and not Xrcc1-dependent DNA repair
    Title: DNA ligase III is critical for mtDNA integrity but not Xrcc1-mediated nuclear DNA repair.
  9. Early embryonic lethality is due to targeted inactivation of DNA ligase III.
    Title: Early embryonic lethality due to targeted inactivation of DNA ligase III.
Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC78176

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA ligase (ATP) activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA ligase (ATP) activity ISO
Inferred from Sequence Orthology
more info
  
enables DNA ligase activity ISO
Inferred from Sequence Orthology
more info
  
enables ligase activity IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables nucleotide binding IEA
Inferred from Electronic Annotation
more info
  
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in DNA biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within DNA damage response IEA
Inferred from Electronic Annotation
more info
  
involved_in DNA ligation ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within DNA recombination IEA
Inferred from Electronic Annotation
more info
  
involved_in DNA recombination IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within DNA repair IEA
Inferred from Electronic Annotation
more info
  
involved_in DNA repair IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within DNA replication IEA
Inferred from Electronic Annotation
more info
  
involved_in base-excision repair, DNA ligation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in base-excision repair, DNA ligation ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within cell cycle IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within cell division IEA
Inferred from Electronic Annotation
more info
  
involved_in double-strand break repair IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in double-strand break repair ISO
Inferred from Sequence Orthology
more info
  
involved_in double-strand break repair via alternative nonhomologous end joining IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in double-strand break repair via alternative nonhomologous end joining ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within double-strand break repair via nonhomologous end joining IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in lagging strand elongation IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within mitochondrial DNA repair IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in mitochondrial DNA repair ISO
Inferred from Sequence Orthology
more info
  
involved_in mitochondrion organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in mitochondrion organization ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within negative regulation of DNA recombination IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of mitochondrial DNA replication ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
part_of DNA ligase III-XRCC1 complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of DNA ligase III-XRCC1 complex ISO
Inferred from Sequence Orthology
more info
  
located_in condensed nuclear chromosome IDA
Inferred from Direct Assay
more info
 PubMed 
located_in mitochondrion ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  
located_in synaptonemal complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
DNA ligase 3
Names
DNA ligase (ATP) 3
DNA ligase III
polydeoxyribonucleotide synthase [ATP] 3
NP_001278174.1
NP_001278175.1
NP_001278176.1
NP_001390785.1
NP_001390786.1
NP_001390787.1
NP_001390788.1
NP_001390789.1
NP_001390790.1
NP_001390791.1
NP_001390792.1
NP_001390793.1
NP_001390794.1
NP_034846.2
XP_006532411.1
XP_006532416.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001291245.2 → NP_001278174.1  DNA ligase 3 isoform a

    See identical proteins and their annotated locations for NP_001278174.1

    Status: VALIDATED

    Source sequence(s)
    AL645594
    Consensus CDS
    CCDS25147.1
    UniProtKB/Swiss-Prot
    E9QL81, P97385, P97386
    UniProtKB/TrEMBL
    Q3U1F0, Q80ZH7
    Related
    ENSMUSP00000133805.2, ENSMUST00000173722.8
    Conserved Domains (3) summary
    TIGR00574
    Location:320 → 832
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:97 → 182
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam16759
    Location:936 → 1007
    LIG3_BRCT; DNA ligase 3 BRCT domain

  2. NM_001291246.2 → NP_001278175.1  DNA ligase 3 isoform b

    See identical proteins and their annotated locations for NP_001278175.1

    Status: VALIDATED

    Source sequence(s)
    AL645594
    Consensus CDS
    CCDS70266.1
    UniProtKB/TrEMBL
    Q3U1F0, Q3UC82
    Related
    ENSMUSP00000134300.2, ENSMUST00000173347.8
    Conserved Domains (6) summary
    cd07967
    Location:687 → 825
    OBF_DNA_ligase_III; The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part of the catalytic core unit
    cd07902
    Location:469 → 681
    Adenylation_DNA_ligase_III; Adenylation domain of DNA Ligase III
    TIGR00574
    Location:319 → 831
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:98 → 178
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam04675
    Location:265 → 430
    DNA_ligase_A_N; DNA ligase N terminus
    pfam16759
    Location:935 → 1006
    LIG3_BRCT; DNA ligase 3 BRCT domain

  3. NM_001291247.2 → NP_001278176.1  DNA ligase 3 isoform b

    See identical proteins and their annotated locations for NP_001278176.1

    Status: VALIDATED

    Source sequence(s)
    AL645594
    Consensus CDS
    CCDS70266.1
    UniProtKB/TrEMBL
    Q3U1F0, Q3UC82
    Related
    ENSMUSP00000133849.2, ENSMUST00000173727.8
    Conserved Domains (6) summary
    cd07967
    Location:687 → 825
    OBF_DNA_ligase_III; The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part of the catalytic core unit
    cd07902
    Location:469 → 681
    Adenylation_DNA_ligase_III; Adenylation domain of DNA Ligase III
    TIGR00574
    Location:319 → 831
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:98 → 178
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam04675
    Location:265 → 430
    DNA_ligase_A_N; DNA ligase N terminus
    pfam16759
    Location:935 → 1006
    LIG3_BRCT; DNA ligase 3 BRCT domain

  4. NM_001403856.1 → NP_001390785.1  DNA ligase 3 isoform a

    Status: VALIDATED

    Source sequence(s)
    AL645594
    UniProtKB/TrEMBL
    Q80ZH7

  5. NM_001403857.1 → NP_001390786.1  DNA ligase 3 isoform a

    Status: VALIDATED

    Source sequence(s)
    AL645594
    UniProtKB/TrEMBL
    Q80ZH7

  6. NM_001403858.1 → NP_001390787.1  DNA ligase 3 isoform b

    Status: VALIDATED

    Source sequence(s)
    AL645594
    UniProtKB/TrEMBL
    Q3UC82

  7. NM_001403859.1 → NP_001390788.1  DNA ligase 3 isoform c

    Status: VALIDATED

    Source sequence(s)
    AL645594

  8. NM_001403860.1 → NP_001390789.1  DNA ligase 3 isoform d

    Status: VALIDATED

    Source sequence(s)
    AL645594

  9. NM_001403861.1 → NP_001390790.1  DNA ligase 3 isoform e

    Status: VALIDATED

    Source sequence(s)
    AL645594

  10. NM_001403862.1 → NP_001390791.1  DNA ligase 3 isoform f

    Status: VALIDATED

    Source sequence(s)
    AL645594

  11. NM_001403863.1 → NP_001390792.1  DNA ligase 3 isoform g

    Status: VALIDATED

    Source sequence(s)
    AL645594
    UniProtKB/TrEMBL
    B1AT03
    Related
    ENSMUSP00000079317.6, ENSMUST00000080461.12

  12. NM_001403864.1 → NP_001390793.1  DNA ligase 3 isoform h

    Status: VALIDATED

    Source sequence(s)
    AL645594

  13. NM_001403865.1 → NP_001390794.1  DNA ligase 3 isoform i

    Status: VALIDATED

    Source sequence(s)
    AL645594

  14. NM_010716.4 → NP_034846.2  DNA ligase 3 isoform a

    See identical proteins and their annotated locations for NP_034846.2

    Status: VALIDATED

    Source sequence(s)
    AL645594
    Consensus CDS
    CCDS25147.1
    UniProtKB/Swiss-Prot
    E9QL81, P97385, P97386
    UniProtKB/TrEMBL
    Q3U1F0, Q80ZH7
    Related
    ENSMUSP00000090525.6, ENSMUST00000092849.12
    Conserved Domains (3) summary
    TIGR00574
    Location:320 → 832
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:97 → 182
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam16759
    Location:936 → 1007
    LIG3_BRCT; DNA ligase 3 BRCT domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000077.7 Reference GRCm39 C57BL/6J

    Range
    82671977..82695100
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006532353.5 → XP_006532416.1  DNA ligase 3 isoform X3

    UniProtKB/Swiss-Prot
    E9QL81, P97385, P97386
    Conserved Domains (2) summary
    TIGR00574
    Location:374 → 886
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:151 → 236
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region

  2. XM_006532348.5 → XP_006532411.1  DNA ligase 3 isoform X2

    UniProtKB/TrEMBL
    Q3U1F0
    Conserved Domains (3) summary
    TIGR00574
    Location:373 → 885
    dnl1; DNA ligase I, ATP-dependent (dnl1)
    pfam00645
    Location:151 → 236
    zf-PARP; Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region
    pfam16759
    Location:989 → 1060
    LIG3_BRCT; DNA ligase 3 BRCT domain

RNA

  1. XR_004936802.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P97386.2 GenPept UniProtKB/Swiss-Prot:P97386

Gene LinkOut

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