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Protein

DNA ligase 4

Gene

LIG4

Organism
Yarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Protein inferred from homologyi

Functioni

Involved in ds DNA break repair. Has a role in non-homologous integration (NHI) pathways where it is required in the final step of non-homologus end-joining.By similarity

Catalytic activityi

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

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei307ATPBy similarity1
Active sitei309N6-AMP-lysine intermediateBy similarity1
Binding sitei314ATPBy similarity1
Binding sitei331ATPBy similarity1
Metal bindingi371Magnesium 1Sequence analysis1
Metal bindingi476Magnesium 2Sequence analysis1
Binding sitei481ATPBy similarity1
Binding sitei492ATPBy similarity1
Binding sitei498ATPBy similarity1

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

DNA damage, DNA recombination, DNA repair, DNA replication

Keywords - Ligandi

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

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligase 4 (EC:6.5.1.1)
Alternative name(s):
DNA ligase IV
Polydeoxyribonucleotide synthase [ATP] 4
Gene namesi
Name:LIG4
Ordered Locus Names:YALI0D21384g
OrganismiYarrowia lipolytica (strain CLIB 122 / E 150) (Yeast) (Candida lipolytica)
Taxonomic identifieri284591 [NCBI]
Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesDipodascaceaeYarrowia
Proteomesi
  • UP000001300 Componenti: Chromosome D

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002783861 – 956DNA ligase 4Add BLAST956

Structurei

3D structure databases

ProteinModelPortaliQ6C8A3.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini700 – 793BRCT 1PROSITE-ProRule annotationAdd BLAST94
Domaini857 – 956BRCT 2PROSITE-ProRule annotationAdd BLAST100

Sequence similaritiesi

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

Keywords - Domaini

Repeat

Phylogenomic databases

HOGENOMiHOG000176213.
InParanoidiQ6C8A3.
KOiK10777.
OMAiHPYEEAT.
OrthoDBiEOG092C18KW.

Family and domain databases

CDDicd00027. BRCT. 1 hit.
Gene3Di3.40.50.10190. 1 hit.
InterProiIPR001357. BRCT_dom.
IPR000977. DNA_ligase_ATP-dep.
IPR012309. DNA_ligase_ATP-dep_C.
IPR012310. DNA_ligase_ATP-dep_cent.
IPR012308. DNA_ligase_ATP-dep_N.
IPR029710. LIG4.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PANTHERiPTHR10459:SF7. PTHR10459:SF7. 1 hit.
PfamiPF16589. BRCT_2. 1 hit.
PF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
[Graphical view]
SMARTiSM00292. BRCT. 2 hits.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 1 hit.
TIGRFAMsiTIGR00574. dnl1. 1 hit.
PROSITEiPS50172. BRCT. 2 hits.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q6C8A3-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSSERRPELE ETAVDPATGS AASRKFSIVQ DAVETTIVAP TNHGPSPRFS
60 70 80 90 100
TLVRNLFEPL VNLSAVVAAL RKKPTEAKAH IASQFIKGWV EEVGKDIYPA
110 120 130 140 150
FRLILPDKDR ERAVYGLKEK ALGRLWVKVL NLAKDSPDAK ALSEWKQGGN
160 170 180 190 200
ESAGNFSKRC YEVLSKRTSL TDYGHMTVDE VNERLDLLAD GETDQAKQIE
210 220 230 240 250
ILTYFYKHMN ATELKWLVNI ILRQMKMNAT EKVFFEPWHP DAESLFNVTA
260 270 280 290 300
SLKRVCWELT DPTKRLTSAE AQVSLFACFM PQIAAFPKYS GQDIAGKHFK
310 320 330 340 350
GRPFYIEEKI DGERMQMHMS EYGNKFHWWS RRSKDFTETY GNSLDDASGS
360 370 380 390 400
LTKRLRGIIN PKVRNCVLDG EMVAYDPATK KIIPFGTLRT ANRNEQNDLN
410 420 430 440 450
LTKPMFMVFD ILLLNDKPLV DYTLAERKRT LRTIFARTDN ETVGQEGVLE
460 470 480 490 500
VLPYTEATTA AEIETCMRKI IAESSEGLVI KDPTSVYRVN TRDDSWLKMK
510 520 530 540 550
PEYMSEFGEK LDVVIIGGYY GSGKRGSILS SYLCGLRADG SDQFWSFFKV
560 570 580 590 600
GGGLTAGDYQ AIRTKTEGKW KRWDKNDKPK NVLLAGPNGD LERPDVWIEP
610 620 630 640 650
SDSVVVEVKA ASVVASDQYK VGLCLRFPRF RALRLDKTWE DGLTISQFAE
660 670 680 690 700
LRQTVEMEAE NKELELEDRK RRNAGPGRGA KRLKLANVSS DEDELGTDER
710 720 730 740 750
PTSVFKATSF AVLSDMSSPR YMSKAAVENL IKKHGGTVFQ TVEGPHTIPV
760 770 780 790 800
ADTRTIKVQA LTKRVHGVDV IRPNWLLDCI NEEKLVALEP RNLLESSAET
810 820 830 840 850
LALAKTNVDE FGDSYTRPLT YKEMQEVLRF MDQFDLDQTN PPDLMMEVLE
860 870 880 890 900
TNDGAVPKGM LFYGKKVYMS TSNMDTVALE TQFRAYDALR CLQFGGANLV
910 920 930 940 950
TDMKDLVVAV AKTEEEAKEL RRVSSEQVFP FRVVSIKWVE ESWKNGTVEI

EDDYPL
Length:956
Mass (Da):108,061
Last modified:August 16, 2004 - v1
Checksum:i5169CFB807F4183B
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CR382130 Genomic DNA. Translation: CAG81303.1.
RefSeqiXP_503109.1. XM_503109.1.

Genome annotation databases

EnsemblFungiiCAG81303; CAG81303; YALI0_D21384g.
GeneIDi2911076.
KEGGiyli:YALI0D21384g.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CR382130 Genomic DNA. Translation: CAG81303.1.
RefSeqiXP_503109.1. XM_503109.1.

3D structure databases

ProteinModelPortaliQ6C8A3.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblFungiiCAG81303; CAG81303; YALI0_D21384g.
GeneIDi2911076.
KEGGiyli:YALI0D21384g.

Phylogenomic databases

HOGENOMiHOG000176213.
InParanoidiQ6C8A3.
KOiK10777.
OMAiHPYEEAT.
OrthoDBiEOG092C18KW.

Family and domain databases

CDDicd00027. BRCT. 1 hit.
Gene3Di3.40.50.10190. 1 hit.
InterProiIPR001357. BRCT_dom.
IPR000977. DNA_ligase_ATP-dep.
IPR012309. DNA_ligase_ATP-dep_C.
IPR012310. DNA_ligase_ATP-dep_cent.
IPR012308. DNA_ligase_ATP-dep_N.
IPR029710. LIG4.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PANTHERiPTHR10459:SF7. PTHR10459:SF7. 1 hit.
PfamiPF16589. BRCT_2. 1 hit.
PF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
[Graphical view]
SMARTiSM00292. BRCT. 2 hits.
[Graphical view]
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 1 hit.
TIGRFAMsiTIGR00574. dnl1. 1 hit.
PROSITEiPS50172. BRCT. 2 hits.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiDNLI4_YARLI
AccessioniPrimary (citable) accession number: Q6C8A3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: February 20, 2007
Last sequence update: August 16, 2004
Last modified: November 30, 2016
This is version 85 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

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

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.