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Protein

DNA ligase 3

Gene

Lig3

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

The alpha isoform interacts with DNA-repair protein XRCC1 and can correct defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents. The beta isoform does not interact with XRCC1 and may be specifically involved in the completion of homologous recombination events that occur during meiotic prophase.

Catalytic activityi

ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).PROSITE-ProRule annotation

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei511 – 5111ATPBy similarity
Active sitei513 – 5131N6-AMP-lysine intermediatePROSITE-ProRule annotationBy similarity
Binding sitei518 – 5181ATPBy similarity
Binding sitei533 – 5331ATPBy similarity
Metal bindingi565 – 5651Magnesium 1By similarity
Metal bindingi660 – 6601Magnesium 2By similarity
Binding sitei665 – 6651ATPBy similarity
Binding sitei676 – 6761ATPBy similarity
Binding sitei680 – 6801ATPBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri94 – 18693PARP-typePROSITE-ProRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

  • base-excision repair, DNA ligation Source: MGI
  • cell cycle Source: UniProtKB-KW
  • cell division Source: UniProtKB-KW
  • DNA biosynthetic process Source: InterPro
  • DNA ligation Source: MGI
  • DNA recombination Source: UniProtKB-KW
  • DNA replication Source: UniProtKB-KW
  • double-strand break repair Source: MGI
  • double-strand break repair via alternative nonhomologous end joining Source: BHF-UCL
  • double-strand break repair via nonhomologous end joining Source: MGI
  • mitochondrial DNA repair Source: MGI
  • mitochondrion organization Source: BHF-UCL
  • negative regulation of DNA recombination Source: MGI
  • negative regulation of mitochondrial DNA replication Source: MGI
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, Zinc

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligase 3 (EC:6.5.1.1)
Alternative name(s):
DNA ligase III
Polydeoxyribonucleotide synthase [ATP] 3
Gene namesi
Name:Lig3
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
Proteomesi
  • UP000000589 Componenti: Unplaced

Organism-specific databases

MGIiMGI:109152. Lig3.

Subcellular locationi

GO - Cellular componenti

  • condensed nuclear chromosome Source: MGI
  • DNA ligase III-XRCC1 complex Source: MGI
  • mitochondrion Source: MGI
  • nucleus Source: MGI
  • synaptonemal complex Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10151015DNA ligase 3PRO_0000059575Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei211 – 2111PhosphoserineCombined sources
Modified residuei228 – 2281PhosphoserineBy similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

EPDiP97386.
MaxQBiP97386.
PaxDbiP97386.
PRIDEiP97386.

PTM databases

iPTMnetiP97386.
PhosphoSiteiP97386.

Expressioni

Tissue specificityi

The alpha isoform is expressed in all tissues, while the beta isoform is expressed only in the testis.

Developmental stagei

During male germ cell differentiation, expression of the beta isoform begins in the later stages of meiotic prophase and ends in the round spermatid stage.

Gene expression databases

BgeeiP97386.
CleanExiMM_LIG3.

Interactioni

Subunit structurei

Interacts (via BRCT domain) with the nuclear DNA-repair protein XRCC1.By similarity

Protein-protein interaction databases

IntActiP97386. 3 interactions.
MINTiMINT-4093266.
STRINGi10090.ENSMUSP00000090525.

Structurei

3D structure databases

ProteinModelPortaliP97386.
SMRiP97386. Positions 89-205, 259-838, 938-1014.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini939 – 101577BRCTPROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni279 – 2824Interaction with DNABy similarity
Regioni323 – 3286Interaction with DNABy similarity
Regioni393 – 3964Interaction with DNABy similarity
Regioni426 – 4327Interaction with DNABy similarity

Domaini

The PARP-type zinc finger is required for DNA ligase activity.By similarity

Sequence similaritiesi

Belongs to the ATP-dependent DNA ligase family.Curated
Contains 1 BRCT domain.PROSITE-ProRule annotation
Contains 1 PARP-type zinc finger.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Zinc fingeri94 – 18693PARP-typePROSITE-ProRule annotationAdd
BLAST

Keywords - Domaini

Zinc-finger

Phylogenomic databases

eggNOGiKOG4437. Eukaryota.
COG1793. LUCA.
HOGENOMiHOG000007653.
HOVERGENiHBG005515.
InParanoidiP97386.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
3.30.1740.10. 1 hit.
3.40.50.10190. 1 hit.
InterProiIPR001357. BRCT_dom.
IPR000977. DNA_ligase_ATP-dep.
IPR012309. DNA_ligase_ATP-dep_C.
IPR012310. DNA_ligase_ATP-dep_cent.
IPR016059. DNA_ligase_ATP-dep_CS.
IPR012308. DNA_ligase_ATP-dep_N.
IPR031916. LIG3_BRCT.
IPR012340. NA-bd_OB-fold.
IPR001510. Znf_PARP.
[Graphical view]
PfamiPF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
PF16759. LIG3_BRCT. 1 hit.
PF00645. zf-PARP. 1 hit.
[Graphical view]
SMARTiSM00292. BRCT. 1 hit.
SM01336. zf-PARP. 1 hit.
[Graphical view]
SUPFAMiSSF117018. SSF117018. 1 hit.
SSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 1 hit.
TIGRFAMsiTIGR00574. dnl1. 1 hit.
PROSITEiPS50172. BRCT. 1 hit.
PS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
PS00347. PARP_ZN_FINGER_1. 1 hit.
PS50064. PARP_ZN_FINGER_2. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform Alpha (identifier: P97386-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MTLAFKILFP RNLCALGRKE LCLFPEQNRW AAISQFSQWS ETNLLGGCCL
60 70 80 90 100
LQRRKPVLAL QRGHLRPRAT HLTFWPGSHV GLCTGPCAMA EQRFCVDYAK
110 120 130 140 150
RGTAGCKKCK EKIVKGVCRI GKVVPNPFSE SGGDMKEWYH IKCMFEKLER
160 170 180 190 200
ARATTKKIED LTELEGWEEL EDNEKEQISQ HIADLSSKAA ATPKKKAAVQ
210 220 230 240 250
AKLTTTGQVT SPVKGASFIT STNPRKFSGF SAAKPNNSEQ APSSPAPGTS
260 270 280 290 300
LSASKCDPKH KDCLLREFRK LCAMVAENPS YNTKTQIIHD FLQKGSTGGF
310 320 330 340 350
SDGFHGDVYL TVKLLLPGVI KSVYNLNDKQ IVKLFSRIFN CNPDDMARDL
360 370 380 390 400
EQGDVSETIR IFFEQSKSFP PAAKSLLTIQ EVDAFLLHLS KLTKEDEQQQ
410 420 430 440 450
ALQDIASRCT ANDLKCIIRL IKHDLKMNSG AKHVLDALDP NAYEAFKASR
460 470 480 490 500
NLQDVVERVL HNEQEVEKDP GRRRALRVQA SLMTPVQPML AEACKSIEYA
510 520 530 540 550
MKKCPNGMFS EIKYDGERVQ VHKKGDHFSY FSRSLKPVLP HKVAHFKDYI
560 570 580 590 600
PKAFPGGQSM ILDSEVLLID NNTGKPLPFG TLGVHKKAAF QDANVCLFVF
610 620 630 640 650
DCIYFNDVSL MDRPLCERRK FLHDNMVEIR NRIMFSEMKQ VTKASDLADM
660 670 680 690 700
INRVIREGLE GLVLKDVKGT YEPGKRHWLK VKKDYLNEGA MADTADLVVL
710 720 730 740 750
GAFYGQGSKG GMMSIFLMGC YDPDSQKWCT VTKCAGGHDD ATLARLQKEL
760 770 780 790 800
VMVKISKDPS KIPSWLKINK IYYPDFIVPD PKKAAVWEIT GAEFSRSEAH
810 820 830 840 850
TADGISIRFP RCTRIRDDKD WKSATNLPQL KELYQLSKDK ADFAVVAGDE
860 870 880 890 900
ASPTTGGSSG ENEGTAGSAG PCKGPPSKSS ASAKTTEQKL NSPSSRGGIK
910 920 930 940 950
PIPKHSPMKP GEKLAVKSSP VKVGMKRKAT DETPCLKKVL LDVFTGVRLY
960 970 980 990 1000
LPPSTPDFKR LKRYFVAFDG DLVQEFDMGS ATHVLGNREK NTDAQLVSSE
1010
WIWACIRKRR LIAPC
Length:1,015
Mass (Da):113,072
Last modified:July 27, 2011 - v2
Checksum:i9CBA3A100C968E77
GO
Isoform Beta (identifier: P97386-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     939-1015: VLLDVFTGVR...IRKRRLIAPC → RRRASRQRGRKAMQTGRR

Show »
Length:956
Mass (Da):106,428
Checksum:iA3F03861053A7EAD
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti299 – 3013GFS → STG in AAC53003 (PubMed:9001252).Curated
Sequence conflicti299 – 3013GFS → STG in AAC53004 (PubMed:9001252).Curated
Sequence conflicti417 – 4171Missing in AAC53003 (PubMed:9001252).Curated
Sequence conflicti417 – 4171Missing in AAC53004 (PubMed:9001252).Curated
Sequence conflicti595 – 5951V → L in AAC53003 (PubMed:9001252).Curated
Sequence conflicti595 – 5951V → L in AAC53004 (PubMed:9001252).Curated
Sequence conflicti702 – 7054AFYG → VFLI in AAC53003 (PubMed:9001252).Curated
Sequence conflicti702 – 7054AFYG → VFLI in AAC53004 (PubMed:9001252).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei939 – 101577VLLDV…LIAPC → RRRASRQRGRKAMQTGRR in isoform Beta. 1 PublicationVSP_001303Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U66058 mRNA. Translation: AAC53004.1.
U66057 mRNA. Translation: AAC53003.1.
AL645594 Genomic DNA. No translation available.
UniGeneiMm.277136.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U66058 mRNA. Translation: AAC53004.1.
U66057 mRNA. Translation: AAC53003.1.
AL645594 Genomic DNA. No translation available.
UniGeneiMm.277136.

3D structure databases

ProteinModelPortaliP97386.
SMRiP97386. Positions 89-205, 259-838, 938-1014.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiP97386. 3 interactions.
MINTiMINT-4093266.
STRINGi10090.ENSMUSP00000090525.

PTM databases

iPTMnetiP97386.
PhosphoSiteiP97386.

Proteomic databases

EPDiP97386.
MaxQBiP97386.
PaxDbiP97386.
PRIDEiP97386.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Organism-specific databases

MGIiMGI:109152. Lig3.

Phylogenomic databases

eggNOGiKOG4437. Eukaryota.
COG1793. LUCA.
HOGENOMiHOG000007653.
HOVERGENiHBG005515.
InParanoidiP97386.

Miscellaneous databases

ChiTaRSiLig3. mouse.
PROiP97386.
SOURCEiSearch...

Gene expression databases

BgeeiP97386.
CleanExiMM_LIG3.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
2.40.50.140. 1 hit.
3.30.1740.10. 1 hit.
3.40.50.10190. 1 hit.
InterProiIPR001357. BRCT_dom.
IPR000977. DNA_ligase_ATP-dep.
IPR012309. DNA_ligase_ATP-dep_C.
IPR012310. DNA_ligase_ATP-dep_cent.
IPR016059. DNA_ligase_ATP-dep_CS.
IPR012308. DNA_ligase_ATP-dep_N.
IPR031916. LIG3_BRCT.
IPR012340. NA-bd_OB-fold.
IPR001510. Znf_PARP.
[Graphical view]
PfamiPF04679. DNA_ligase_A_C. 1 hit.
PF01068. DNA_ligase_A_M. 1 hit.
PF04675. DNA_ligase_A_N. 1 hit.
PF16759. LIG3_BRCT. 1 hit.
PF00645. zf-PARP. 1 hit.
[Graphical view]
SMARTiSM00292. BRCT. 1 hit.
SM01336. zf-PARP. 1 hit.
[Graphical view]
SUPFAMiSSF117018. SSF117018. 1 hit.
SSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 1 hit.
TIGRFAMsiTIGR00574. dnl1. 1 hit.
PROSITEiPS50172. BRCT. 1 hit.
PS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
PS00347. PARP_ZN_FINGER_1. 1 hit.
PS50064. PARP_ZN_FINGER_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "An alternative splicing event which occurs in mouse pachytene spermatocytes generates a form of DNA ligase III with distinct biochemical properties that may function in meiotic recombination."
    Mackey Z.B., Ramos W., Levin D.S., Walter C.A., McCarrey J.R., Tomkinson A.E.
    Mol. Cell. Biol. 17:989-998(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS ALPHA AND BETA).
    Tissue: Testis.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  3. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-211, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.
  4. "The phagosomal proteome in interferon-gamma-activated macrophages."
    Trost M., English L., Lemieux S., Courcelles M., Desjardins M., Thibault P.
    Immunity 30:143-154(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-211, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  5. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-211, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Spleen and Testis.

Entry informationi

Entry nameiDNLI3_MOUSE
AccessioniPrimary (citable) accession number: P97386
Secondary accession number(s): E9QL81, P97385
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 15, 1998
Last sequence update: July 27, 2011
Last modified: May 11, 2016
This is version 145 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. 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.