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Protein

DNA ligase 4

Gene

DNL4

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Has minor DNA joining activity. Can act on oligo(PDT)/poly(rA) substrate.

Catalytic activityi

ATP + (deoxyribonucleotide)(n)-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP + diphosphate.PROSITE-ProRule annotation

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei280ATPBy similarity1
Active sitei282N6-AMP-lysine intermediatePROSITE-ProRule annotation1
Binding sitei287ATPBy similarity1
Binding sitei304ATPBy similarity1
Metal bindingi340Magnesium 1Sequence analysis1
Metal bindingi442Magnesium 2Sequence analysis1
Binding sitei447ATPBy similarity1
Binding sitei458ATPBy similarity1
Binding sitei464ATPBy similarity1

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • DNA binding Source: InterPro
  • DNA ligase (ATP) activity Source: SGD
  • metal ion binding Source: UniProtKB-KW

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Cell cycle, Cell division, DNA damage, DNA recombination, DNA repair, DNA replication

Keywords - Ligandi

ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciYEAST:G3O-33555-MONOMER.
BRENDAi6.5.1.1. 984.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligase 4 (EC:6.5.1.1PROSITE-ProRule annotation)
Alternative name(s):
DNA ligase II
DNA ligase IV
Polydeoxyribonucleotide synthase [ATP] 4
Gene namesi
Name:DNL4
Synonyms:LIG4
Ordered Locus Names:YOR005C
ORF Names:UND407, UNE452
OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Taxonomic identifieri559292 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
Proteomesi
  • UP000002311 Componenti: Chromosome XV

Organism-specific databases

EuPathDBiFungiDB:YOR005C.
SGDiS000005531. DNL4.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: GO_Central
  • DNA ligase IV complex Source: SGD
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000595821 – 944DNA ligase 4Add BLAST944

Proteomic databases

PRIDEiQ08387.

PTM databases

iPTMnetiQ08387.

Interactioni

Subunit structurei

Interacts with LIF1 via its BRCT domain. Interacts with POL4 in the DNL4-LIF1 complex.3 Publications

Protein-protein interaction databases

BioGridi34408. 50 interactors.
DIPiDIP-5801N.
IntActiQ08387. 1 interactor.
MINTiMINT-672762.

Structurei

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1Z56X-ray3.92C681-943[»]
ProteinModelPortaliQ08387.
SMRiQ08387.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ08387.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini681 – 780BRCT 1PROSITE-ProRule annotationAdd BLAST100
Domaini836 – 941BRCT 2PROSITE-ProRule annotationAdd BLAST106

Sequence similaritiesi

Belongs to the ATP-dependent DNA ligase family.Curated
Contains 2 BRCT domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

GeneTreeiENSGT00860000133881.
HOGENOMiHOG000093622.
InParanoidiQ08387.
KOiK10777.
OMAiHSINENC.
OrthoDBiEOG092C18KW.

Family and domain databases

CDDicd00027. BRCT. 1 hit.
Gene3Di3.40.50.10190. 1 hit.
InterProiIPR001357. BRCT_dom.
IPR000977. DNA_ligase_ATP-dep.
IPR012310. DNA_ligase_ATP-dep_cent.
IPR016059. DNA_ligase_ATP-dep_CS.
IPR012308. DNA_ligase_ATP-dep_N.
IPR029710. LIG4.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PANTHERiPTHR10459:SF7. PTHR10459:SF7. 2 hits.
PfamiPF00533. BRCT. 2 hits.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
[Graphical view]
SMARTiSM00292. BRCT. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 2 hits.
SSF52113. SSF52113. 3 hits.
TIGRFAMsiTIGR00574. dnl1. 1 hit.
PROSITEiPS50172. BRCT. 2 hits.
PS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q08387-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MISALDSIPE PQNFAPSPDF KWLCEELFVK IHEVQINGTA GTGKSRSFKY
60 70 80 90 100
YEIISNFVEM WRKTVGNNIY PALVLALPYR DRRIYNIKDY VLIRTICSYL
110 120 130 140 150
KLPKNSATEQ RLKDWKQRVG KGGNLSSLLV EEIAKRRAEP SSKAITIDNV
160 170 180 190 200
NHYLDSLSGD RFASGRGFKS LVKSKPFLHC VENMSFVELK YFFDIVLKNR
210 220 230 240 250
VIGGQEHKLL NCWHPDAQDY LSVISDLKVV TSKLYDPKVR LKDDDLSIKV
260 270 280 290 300
GFAFAPQLAK KVNLSYEKIC RTLHDDFLVE EKMDGERIQV HYMNYGESIK
310 320 330 340 350
FFSRRGIDYT YLYGASLSSG TISQHLRFTD SVKECVLDGE MVTFDAKRRV
360 370 380 390 400
ILPFGLVKGS AKEALSFNSI NNVDFHPLYM VFDLLYLNGT SLTPLPLHQR
410 420 430 440 450
KQYLNSILSP LKNIVEIVRS SRCYGVESIK KSLEVAISLG SEGVVLKYYN
460 470 480 490 500
SSYNVASRNN NWIKVKPEYL EEFGENLDLI VIGRDSGKKD SFMLGLLVLD
510 520 530 540 550
EEEYKKHQGD SSEIVDHSSQ EKHIQNSRRR VKKILSFCSI ANGISQEEFK
560 570 580 590 600
EIDRKTRGHW KRTSEVAPPA SILEFGSKIP AEWIDPSESI VLEIKSRSLD
610 620 630 640 650
NTETNMQKYA TNCTLYGGYC KRIRYDKEWT DCYTLNDLYE SRTVKSNPSY
660 670 680 690 700
QAERSQLGLI RKKRKRVLIS DSFHQNRKQL PISNIFAGLL FYVLSDYVTE
710 720 730 740 750
DTGIRITRAE LEKTIVEHGG KLIYNVILKR HSIGDVRLIS CKTTTECKAL
760 770 780 790 800
IDRGYDILHP NWVLDCIAYK RLILIEPNYC FNVSQKMRAV AEKRVDCLGD
810 820 830 840 850
SFENDISETK LSSLYKSQLS LPPMGELEID SEVRRFPLFL FSNRIAYVPR
860 870 880 890 900
RKISTEDDII EMKIKLFGGK ITDQQSLCNL IIIPYTDPIL RKDCMNEVHE
910 920 930 940
KIKEQIKASD TIPKIARVVA PEWVDHSINE NCQVPEEDFP VVNY
Length:944
Mass (Da):108,515
Last modified:November 1, 1996 - v1
Checksum:i7FB6D7927E1719B5
GO

Sequence cautioni

The sequence AAC49484 differs from that shown. Reason: Frameshift at positions 408 and 413. Produces 2 separate ORFs.Curated
The sequence AAC49485 differs from that shown. Reason: Frameshift at positions 408 and 413. Produces 2 separate ORFs.Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U43491 Genomic DNA. Translation: AAC49485.1. Frameshift.
U43491 Genomic DNA. Translation: AAC49484.1. Frameshift.
Z74913 Genomic DNA. Translation: CAA99193.1.
BK006948 Genomic DNA. Translation: DAA10787.1.
PIRiS66870.
RefSeqiNP_014647.1. NM_001183424.1.

Genome annotation databases

EnsemblFungiiYOR005C; YOR005C; YOR005C.
GeneIDi854166.
KEGGisce:YOR005C.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U43491 Genomic DNA. Translation: AAC49485.1. Frameshift.
U43491 Genomic DNA. Translation: AAC49484.1. Frameshift.
Z74913 Genomic DNA. Translation: CAA99193.1.
BK006948 Genomic DNA. Translation: DAA10787.1.
PIRiS66870.
RefSeqiNP_014647.1. NM_001183424.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1Z56X-ray3.92C681-943[»]
ProteinModelPortaliQ08387.
SMRiQ08387.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi34408. 50 interactors.
DIPiDIP-5801N.
IntActiQ08387. 1 interactor.
MINTiMINT-672762.

PTM databases

iPTMnetiQ08387.

Proteomic databases

PRIDEiQ08387.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiYOR005C; YOR005C; YOR005C.
GeneIDi854166.
KEGGisce:YOR005C.

Organism-specific databases

EuPathDBiFungiDB:YOR005C.
SGDiS000005531. DNL4.

Phylogenomic databases

GeneTreeiENSGT00860000133881.
HOGENOMiHOG000093622.
InParanoidiQ08387.
KOiK10777.
OMAiHSINENC.
OrthoDBiEOG092C18KW.

Enzyme and pathway databases

BioCyciYEAST:G3O-33555-MONOMER.
BRENDAi6.5.1.1. 984.

Miscellaneous databases

EvolutionaryTraceiQ08387.
PROiQ08387.

Family and domain databases

CDDicd00027. BRCT. 1 hit.
Gene3Di3.40.50.10190. 1 hit.
InterProiIPR001357. BRCT_dom.
IPR000977. DNA_ligase_ATP-dep.
IPR012310. DNA_ligase_ATP-dep_cent.
IPR016059. DNA_ligase_ATP-dep_CS.
IPR012308. DNA_ligase_ATP-dep_N.
IPR029710. LIG4.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PANTHERiPTHR10459:SF7. PTHR10459:SF7. 2 hits.
PfamiPF00533. BRCT. 2 hits.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
[Graphical view]
SMARTiSM00292. BRCT. 1 hit.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 2 hits.
SSF52113. SSF52113. 3 hits.
TIGRFAMsiTIGR00574. dnl1. 1 hit.
PROSITEiPS50172. BRCT. 2 hits.
PS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDNLI4_YEAST
AccessioniPrimary (citable) accession number: Q08387
Secondary accession number(s): D6W271, Q02913, Q02914
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: November 30, 2016
This is version 150 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programFungal Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. Yeast
    Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
  4. Yeast chromosome XV
    Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.