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Protein

DNA ligase 4

Gene

DNL4

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed-Annotation score: -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

Keywordsi

Molecular functionLigase
Biological processCell cycle, Cell division, DNA damage, DNA recombination, DNA repair, DNA replication
LigandATP-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

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

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

Proteomic databases

PaxDbiQ08387
PRIDEiQ08387

PTM databases

iPTMnetiQ08387

Interactioni

Subunit structurei

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

Binary interactionsi

WithEntry#Exp.IntActNotes
LIF1P531503EBI-5983,EBI-23865

Protein-protein interaction databases

BioGridi34408, 250 interactors
ComplexPortaliCPX-1665 DNA ligase IV complex
DIPiDIP-5801N
IntActiQ08387, 23 interactors
STRINGi4932.YOR005C

Structurei

3D structure databases

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

Keywords - Domaini

Repeat

Phylogenomic databases

GeneTreeiENSGT00860000133881
HOGENOMiHOG000093622
InParanoidiQ08387
KOiK10777
OMAiHMCPSTK
OrthoDBiEOG092C18KW

Family and domain databases

CDDicd00027 BRCT, 1 hit
Gene3Di1.10.3260.10, 1 hit
3.40.50.10190, 2 hits
InterProiView protein in InterPro
IPR001357 BRCT_dom
IPR036420 BRCT_dom_sf
IPR000977 DNA_ligase_ATP-dep
IPR012310 DNA_ligase_ATP-dep_cent
IPR016059 DNA_ligase_ATP-dep_CS
IPR012308 DNA_ligase_ATP-dep_N
IPR036599 DNA_ligase_N_sf
IPR029710 LIG4
IPR012340 NA-bd_OB-fold
PANTHERiPTHR10459:SF7 PTHR10459:SF7, 1 hit
PfamiView protein in Pfam
PF00533 BRCT, 2 hits
PF01068 DNA_ligase_A_M, 1 hit
PF04675 DNA_ligase_A_N, 1 hit
SMARTiView protein in SMART
SM00292 BRCT, 1 hit
SUPFAMiSSF50249 SSF50249, 2 hits
SSF52113 SSF52113, 3 hits
TIGRFAMsiTIGR00574 dnl1, 1 hit
PROSITEiView protein in PROSITE
PS50172 BRCT, 2 hits
PS00697 DNA_LIGASE_A1, 1 hit
PS00333 DNA_LIGASE_A2, 1 hit
PS50160 DNA_LIGASE_A3, 1 hit

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

Similar proteinsi

Entry informationi

Entry nameiDNLI4_YEAST
AccessioniPrimary (citable) accession number: Q08387
Secondary accession number(s): D6W271, Q02913, Q02914
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: July 18, 2018
This is version 164 of the entry and version 1 of the sequence. See 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

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