Tbio LIG3 DNA ligase 3

Protein Summary

Description

Isoform 3 functions as heterodimer with DNA-repair protein XRCC1 in the nucleus and can correct defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents. Isoform 1 is targeted to mitochondria, where it functions as DNA ligase in mitochondrial base-excision DNA repair (PubMed:10207110, PubMed:24674627). This gene is a member of the DNA ligase family. Each member of this family encodes a protein that catalyzes the joining of DNA ends but they each have a distinct role in DNA metabolism. The protein encoded by this gene is involved in excision repair and is located in both the mitochondria and nucleus, with translation initiation from the upstream start codon allowing for transport to the mitochondria and translation initiation from a downstream start codon allowing for transport to the nucleus. Additionally, alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]

Uniprot Accession IDs

• P49916
• E5KLB5
• E5KLB6
• Q16714
• Q6NVK3

Gene Name

• LIG3

Ensembl ID

• ENST00000262327
• ENSP00000262327
• ENSG00000005156
• ENST00000378526
• ENSP00000367787

Symbol

• LIG2
• LIG3alpha

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
drug perturbation	0.99
protein domain	0.97
molecular function	0.96
transcription factor perturbation	0.94
kinase perturbation	0.93

Protein Classes

PANTHER Classes

Protein / Nucleic Acid Binding / Dna Binding Protein / Dna Ligase / Dna Ligase 3

Protein / Ligase / Dna Ligase / Dna Ligase 3

DTO Classes

Protein / Enzyme / Ligase / Dna Ligase / Dna Ligase 3

IDG Development Level Summary

Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 90.32   (req: < 5)

Gene RIFs: 36   (req: <= 3)

Antibodies: 313   (req: <= 50)

Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 90.32   (req: >= 5)

Gene RIFs: 36   (req: > 3)

Antibodies: 313   (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 19

Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 0

Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0

Protein Sequence and Structure

Residue Counts

Protein Sequence

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Expression Data (0 Tissues)

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No expression data found

Related Tools

Target Illumination GWAS Analytics (TIGA)

TIGA scores and ranks GWAS discovered associations according to the quantity and quality of the evidence supporting the association.

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GENEVA

GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.

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GlyGen

GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.

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ARCHS4

ARCHS4 provides access to gene-function predictions based on RNA-seq co-expression, and gene expression levels across cell and tissues.

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Approved Drugs (0)

No approved drugs found

Active Ligands (0)

No active ligands found

Protein-Protein Interactions (194)

Explore Interacting Targets

1 – 10 of 194

• See Interactions on String-DB

POLB

Tchem

Family:  Enzyme

Novelty:  0.00145102

p_int:  0.999999993

p_ni:  6e-9

p_wrong:  1e-9

Score:  0.989

Data Source:  BioPlex,Reactome,STRINGDB

APLF

Tbio

Novelty:  0.01347476

p_int:  0.999999909

p_ni:  9.1e-8

Score:  0.766

Data Source:  BioPlex,STRINGDB

CALML3

Tbio

Novelty:  0.0336689

p_int:  0.99980266

p_ni:  0.00019734

Data Source:  BioPlex

JMJD4

Tbio

Novelty:  0.09951585

p_int:  0.999785071

p_ni:  0.000214928

p_wrong:  1e-9

Data Source:  BioPlex

HIST1H2BA

Tbio

Novelty:  0.02431803

p_int:  0.999545992

p_ni:  0.000454008

Score:  0.162

Data Source:  BioPlex,STRINGDB

H2AFX

Tbio

Novelty:  0.00048694

p_int:  0.999460209

p_ni:  0.000539791

Score:  0.498

Data Source:  BioPlex,STRINGDB

RNF146

Tbio

Family:  Enzyme

Novelty:  0.05463359

p_int:  0.998491396

p_ni:  0.001508604

Score:  0.356

Data Source:  BioPlex,STRINGDB

XRCC6

Tbio

Novelty:  0.00127955

p_int:  0.998437614

p_ni:  0.001562386

Score:  0.951

Data Source:  BioPlex,STRINGDB

RPA2

Tbio

Novelty:  0.00879115

p_int:  0.997587246

p_ni:  0.002412753

p_wrong:  1e-9

Score:  0.946

Data Source:  BioPlex,Reactome,STRINGDB

FMC1

Tbio

Novelty:  0.06702205

p_int:  0.996180801

p_ni:  0.001664718

p_wrong:  0.002154482

Score:  0.224

Data Source:  BioPlex,STRINGDB

Nearest Tclin Targets

Nearest Tclin calculations are only available for targets with KEGG Pathway annotations.

Pathways (14)

Reactome (13)

KEGG (1)

APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway (R-HSA-5649702)

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5

1 – 5 of 13

Data Source	Name	Explore in Pharos	Explore in Source
Reactome	APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway	7 targets	R-HSA-5649702
Reactome	Base Excision Repair	72 targets	R-HSA-73884
Reactome	DNA Double-Strand Break Repair	146 targets	R-HSA-5693532
Reactome	DNA Repair	306 targets	R-HSA-73894
Reactome	Gap-filling DNA repair synthesis and ligation in GG-NER	25 targets	R-HSA-5696397

Name	Explore in Pharos	Explore in Source
APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway	7 targets	R-HSA-5649702
Base Excision Repair	72 targets	R-HSA-73884
DNA Double-Strand Break Repair	146 targets	R-HSA-5693532
DNA Repair	306 targets	R-HSA-73894
Gap-filling DNA repair synthesis and ligation in GG-NER	25 targets	R-HSA-5696397

Viral Interactions (0)

No viral interactions found

Gene Ontology Terms (24)

Functions (5)

Components (5)

Processes (14)

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1 – 5 of 5

GO Term	Evidence	Assigned by
DNA ligase (ATP) activity	Inferred from Direct Assay (IDA)	BHF-UCL
DNA ligase activity	Inferred from Direct Assay (IDA)	BHF-UCL
ATP binding	Inferred from Electronic Annotation (IEA)	UniProtKB-KW
DNA binding	Inferred from Electronic Annotation (IEA)	InterPro
zinc ion binding	Inferred from Electronic Annotation (IEA)	InterPro

Disease Associations ()

No disease associations found

GWAS Traits (5)

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5

1 – 5 of 5

GWAS Trait	EFO ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
QT interval	EFO_0004682	2	1	0	1.2	57.8
macrophage inflammatory protein 1b measurement	EFO_0008219	1	1	1		48.5
pulse pressure measurement	EFO_0005763	1	1	1		45.7
electrocardiography	EFO_0004327	1	1	17		40.7
TPE interval measurement	EFO_0004644	1	1	1		21.5

• Explore on Target Illumination GWAS Analytics (TIGA)

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5

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GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)	Provenance
QT interval	EFO_0004682	0	1.2	57.8
macrophage inflammatory protein 1b measurement	EFO_0008219	1		48.5
pulse pressure measurement	EFO_0005763	1		45.7
electrocardiography	EFO_0004327	17		40.7
TPE interval measurement	EFO_0004644	1		21.5

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UniProt Keyword Find Similar Targets

No Header	No Header
3D-structure
Alternative initiation
Alternative splicing
ATP-binding
Cell cycle
Cell division
Complete proteome
DNA damage
DNA recombination
DNA repair

GWAS Trait Find Similar Targets

No Header	No Header
electrocardiography
macrophage inflammatory protein 1b measurement
pulse pressure measurement
QT interval
TPE interval measurement

MGI Phenotype Find Similar Targets

No Header	No Header
behavior/neurological phenotype
cardiovascular system phenotype
cellular phenotype
embryo phenotype
growth/size/body region phenotype
homeostasis/metabolism phenotype
mortality/aging
muscle phenotype
nervous system phenotype

IDG Resources

No IDG generated resources found

Orthologs (12)

1 – 5 of 12

Species	Name	Source ID	Gene ID	OMA	EggNOG	Inparanoid
Chimp	DNA ligase 3	VGNC:9437	454581
Macaque	DNA ligase 3		715181
Mouse	ligase III, DNA, ATP-dependent	MGI:109152	16882
Rat	DNA ligase 3	RGD:1309875	303369
Dog	DNA ligase 3	VGNC:42674	491145

Species	Name	OMA	EggNOG	Inparanoid
Chimp	DNA ligase 3
Macaque	DNA ligase 3
Mouse	ligase III, DNA, ATP-dependent
Rat	DNA ligase 3
Dog	DNA ligase 3

Publication Statistics

PubMed Score 90.32

PubMed score by year

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PubTator Score 82.53

PubTator score by year

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Related Publications

Text Mined References (82)

GeneRif Annotations (36)

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PMID	Year	Title