DNL4 DNA ligase (ATP) DNL4 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Gene symbol: DNL4
Gene description: DNA ligase (ATP) DNL4
Primary source: FungiDB:YOR005C
Locus tag: YOR005C
See related: SGD:S000005531; AllianceGenome:SGD:S000005531
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Also known as: LIG4
Summary: Enables DNA ligase (ATP) activity. Involved in double-strand break repair via nonhomologous end joining and maintenance of rDNA. Part of DNA ligase IV complex. Human ortholog(s) of this gene implicated in several diseases, including DNA ligase IV deficiency; colorectal cancer; high grade glioma; multiple myeloma; and prostate cancer. Orthologous to human LIG4 (DNA ligase 4). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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See DNL4 in Genome Data Viewer

Location:: chromosome: XV

Exon count:: 1

Sequence:: Chromosome: XV; NC_001147.6 (334509..337343, complement)

Chromosome XV - NC_001147.6 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001147.6

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

This study also uncovered an important role for Rev3 and Rev7 (but not for Pol32) subunits of polymerase z in the survival of cells undergoing telomere losses and forming palindromes
Title: Telomere Dysfunction Triggers Palindrome Formation Independently of Double-Strand Break Repair Mechanisms.
Dnl4 BRCT1 domain supports DNA double-strand breaks recruitment and NHEJ in a manner distinct from Lif1 binding and reveal a complexity of Dnl4 BRCT domain functions in support of stable DNA double-strand breaks association.
Title: Yeast DNA ligase IV mutations reveal a nonhomologous end joining function of BRCT1 distinct from XRCC4/Lif1 binding.
These findings indicate that Dnl4 can promote mutagenic end joining independently of its catalytic activity, likely by a mechanism that involves Cdc9.
Title: Saccharomyces cerevisiae DNA ligase IV supports imprecise end joining independently of its catalytic activity.
lack of DNL4 rescues the short chronologic life span of the yme1 mutant.
Title: Accumulation of linear mitochondrial DNA fragments in the nucleus shortens the chronological life span of yeast.
Consistently, dnl4 cells displayed altered fork structures at the replication fork barrier, leading us to propose an as yet unrecognized role for Dnl4 in the maintenance of ribosomal DNA stability.
Title: DNA ligase 4 stabilizes the ribosomal DNA array upon fork collapse at the replication fork barrier.
Data show that a lack of any of the NHEJ proteins Yku (Yku70-Yku80), Lif1 or DNA ligase IV (Dnl4) increases 5' DSB end degradation in G1 phase, with ykuDelta cells showing the strongest effect.
Title: The Yku70-Yku80 complex contributes to regulate double-strand break processing and checkpoint activation during the cell cycle.
Dnl4 mutation suppressed elevated levels of chromosome loss and telomere fusion associated with mono-allelic expression of MAT.
Title: Mating type influences chromosome loss and replicative senescence in telomerase-deficient budding yeast by Dnl4-dependent telomere fusion.
Dnl4-Lif1 plays an important part in determining repair pathway choice by participating at an early stage of DSB engagement in addition to providing the DNA ligase activity that completes nonhomologous end joining.
Title: Role of Dnl4-Lif1 in nonhomologous end-joining repair complex assembly and suppression of homologous recombination.
Results describe a series of pair-wise interactions among FEN-1, Pol4 and Dnl4, the factors that complete the repair of DNA double-strand breaks by non-homologous end-joining.
Title: Processing and joining of DNA ends coordinated by interactions among Dnl4/Lif1, Pol4, and FEN-1.

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables ATP binding	IBA Inferred from Biological aspect of Ancestor more info
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables DNA binding	IBA Inferred from Biological aspect of Ancestor 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	IDA Inferred from Direct Assay more info	PubMed
enables DNA ligase (ATP) activity	IEA Inferred from Electronic Annotation more info
enables DNA ligase (ATP) activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables ligase activity	IEA Inferred from Electronic Annotation more info
enables metal 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
involved_in DNA ligation involved in DNA repair	IEA Inferred from Electronic Annotation more info
involved_in DNA recombination	IEA Inferred from Electronic Annotation more info
involved_in DNA repair	IEA Inferred from Electronic Annotation more info
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in double-strand break repair via nonhomologous end joining	IBA Inferred from Biological aspect of Ancestor more info
involved_in double-strand break repair via nonhomologous end joining	IDA Inferred from Direct Assay more info	PubMed
involved_in double-strand break repair via nonhomologous end joining	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in maintenance of rDNA	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nucleotide-excision repair, DNA gap filling	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of DNA ligase IV complex	IBA Inferred from Biological aspect of Ancestor more info
part_of DNA ligase IV complex	IPI Inferred from Physical Interaction more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: DNA ligase (ATP) DNL4

NP_014647.1

EC 6.5.1.1

DNA ligase required for nonhomologous end-joining (NHEJ); forms stable heterodimer with required cofactor Lif1p, interacts with Nej1p; involved in meiosis, not essential for vegetative growth; mutations in human ortholog lead to ligase IV syndrome and Dubowitz syndrome

NCBI Reference Sequences (RefSeq)

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Genome Annotation

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

Reference assembly

Genomic

NC_001147.6 Reference assembly

Range

334509..337343 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001183424.1 → NP_014647.1 TPA: DNA ligase (ATP) DNL4 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_014647.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6W271, Q02913, Q02914, Q08387

UniProtKB/TrEMBL

A6ZNL0, B5VRQ7, C7GJU8, C8ZHW8

Conserved Domains (5) summary

cd07968
Location:474 → 635

OBF_DNA_ligase_IV; The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase IV is a DNA-binding module that is part of the catalytic core unit

cd07903
Location:244 → 471

Adenylation_DNA_ligase_IV; Adenylation domain of DNA Ligase IV

TIGR00574
Location:84 → 717

dnl1; DNA ligase I, ATP-dependent (dnl1)

pfam00533
Location:681 → 767

BRCT; BRCA1 C Terminus (BRCT) domain

pfam04675
Location:20 → 207

DNA_ligase_A_N; DNA ligase N terminus