DNLI3_MOUSE
ID DNLI3_MOUSE Reviewed; 1015 AA.
AC P97386; E9QL81; P97385;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 27-JUL-2011, sequence version 2.
DT 03-AUG-2022, entry version 175.
DE RecName: Full=DNA ligase 3;
DE EC=6.5.1.1 {ECO:0000255|PROSITE-ProRule:PRU10135};
DE AltName: Full=DNA ligase III;
DE AltName: Full=Polydeoxyribonucleotide synthase [ATP] 3;
GN Name=Lig3;
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS ALPHA AND BETA).
RC TISSUE=Testis;
RX PubMed=9001252; DOI=10.1128/mcb.17.2.989;
RA Mackey Z.B., Ramos W., Levin D.S., Walter C.A., McCarrey J.R.,
RA Tomkinson A.E.;
RT "An alternative splicing event which occurs in mouse pachytene
RT spermatocytes generates a form of DNA ligase III with distinct biochemical
RT properties that may function in meiotic recombination.";
RL Mol. Cell. Biol. 17:989-998(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C57BL/6J;
RX PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
RA Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X.,
RA Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y.,
RA Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S.,
RA Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R.,
RA Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K.,
RA Eichler E.E., Ponting C.P.;
RT "Lineage-specific biology revealed by a finished genome assembly of the
RT mouse.";
RL PLoS Biol. 7:E1000112-E1000112(2009).
RN [3]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-211, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Liver;
RX PubMed=17242355; DOI=10.1073/pnas.0609836104;
RA Villen J., Beausoleil S.A., Gerber S.A., Gygi S.P.;
RT "Large-scale phosphorylation analysis of mouse liver.";
RL Proc. Natl. Acad. Sci. U.S.A. 104:1488-1493(2007).
RN [4]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-211, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19144319; DOI=10.1016/j.immuni.2008.11.006;
RA Trost M., English L., Lemieux S., Courcelles M., Desjardins M.,
RA Thibault P.;
RT "The phagosomal proteome in interferon-gamma-activated macrophages.";
RL Immunity 30:143-154(2009).
RN [5]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-211, AND IDENTIFICATION BY
RP MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Spleen, and Testis;
RX PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL Cell 143:1174-1189(2010).
CC -!- FUNCTION: The alpha isoform interacts with DNA-repair protein XRCC1 and
CC can correct defective DNA strand-break repair and sister chromatid
CC exchange following treatment with ionizing radiation and alkylating
CC agents. The beta isoform does not interact with XRCC1 and may be
CC specifically involved in the completion of homologous recombination
CC events that occur during meiotic prophase.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + (deoxyribonucleotide)n-3'-hydroxyl + 5'-phospho-
CC (deoxyribonucleotide)m = (deoxyribonucleotide)n+m + AMP +
CC diphosphate.; EC=6.5.1.1; Evidence={ECO:0000255|PROSITE-
CC ProRule:PRU10135};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC -!- SUBUNIT: Interacts (via BRCT domain) with the nuclear DNA-repair
CC protein XRCC1. {ECO:0000250|UniProtKB:P49916}.
CC -!- SUBCELLULAR LOCATION: Nucleus.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=Alpha;
CC IsoId=P97386-1; Sequence=Displayed;
CC Name=Beta;
CC IsoId=P97386-2; Sequence=VSP_001303;
CC -!- TISSUE SPECIFICITY: The alpha isoform is expressed in all tissues,
CC while the beta isoform is expressed only in the testis.
CC -!- DEVELOPMENTAL STAGE: During male germ cell differentiation, expression
CC of the beta isoform begins in the later stages of meiotic prophase and
CC ends in the round spermatid stage.
CC -!- DOMAIN: The PARP-type zinc finger is required for DNA ligase activity.
CC {ECO:0000250|UniProtKB:P49916}.
CC -!- SIMILARITY: Belongs to the ATP-dependent DNA ligase family.
CC {ECO:0000305}.
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DR EMBL; U66058; AAC53004.1; -; mRNA.
DR EMBL; U66057; AAC53003.1; -; mRNA.
DR EMBL; AL645594; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR AlphaFoldDB; P97386; -.
DR BMRB; P97386; -.
DR SMR; P97386; -.
DR CORUM; P97386; -.
DR IntAct; P97386; 2.
DR STRING; 10090.ENSMUSP00000090525; -.
DR iPTMnet; P97386; -.
DR PhosphoSitePlus; P97386; -.
DR EPD; P97386; -.
DR jPOST; P97386; -.
DR MaxQB; P97386; -.
DR PaxDb; P97386; -.
DR PeptideAtlas; P97386; -.
DR PRIDE; P97386; -.
DR ProteomicsDB; 277355; -. [P97386-1]
DR ProteomicsDB; 277356; -. [P97386-2]
DR MGI; MGI:109152; Lig3.
DR eggNOG; KOG4437; Eukaryota.
DR InParanoid; P97386; -.
DR Reactome; R-MMU-110381; Resolution of AP sites via the single-nucleotide replacement pathway.
DR Reactome; R-MMU-5649702; APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway.
DR Reactome; R-MMU-5685939; HDR through MMEJ (alt-NHEJ).
DR Reactome; R-MMU-6782210; Gap-filling DNA repair synthesis and ligation in TC-NER.
DR ChiTaRS; Lig3; mouse.
DR PRO; PR:P97386; -.
DR Proteomes; UP000000589; Unplaced.
DR RNAct; P97386; protein.
DR GO; GO:0000794; C:condensed nuclear chromosome; IDA:MGI.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0070421; C:DNA ligase III-XRCC1 complex; ISO:MGI.
DR GO; GO:0005739; C:mitochondrion; ISO:MGI.
DR GO; GO:0005654; C:nucleoplasm; ISO:MGI.
DR GO; GO:0005634; C:nucleus; ISO:MGI.
DR GO; GO:0000795; C:synaptonemal complex; IDA:MGI.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0003677; F:DNA binding; IEA:InterPro.
DR GO; GO:0003910; F:DNA ligase (ATP) activity; ISO:MGI.
DR GO; GO:0003909; F:DNA ligase activity; ISO:MGI.
DR GO; GO:0008270; F:zinc ion binding; IEA:InterPro.
DR GO; GO:0006288; P:base-excision repair, DNA ligation; ISO:MGI.
DR GO; GO:0007049; P:cell cycle; IEA:UniProtKB-KW.
DR GO; GO:0051301; P:cell division; IEA:UniProtKB-KW.
DR GO; GO:0071897; P:DNA biosynthetic process; IEA:InterPro.
DR GO; GO:0006266; P:DNA ligation; ISO:MGI.
DR GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR GO; GO:0006302; P:double-strand break repair; ISO:MGI.
DR GO; GO:0097681; P:double-strand break repair via alternative nonhomologous end joining; IMP:BHF-UCL.
DR GO; GO:0006303; P:double-strand break repair via nonhomologous end joining; IMP:MGI.
DR GO; GO:0006273; P:lagging strand elongation; IBA:GO_Central.
DR GO; GO:0043504; P:mitochondrial DNA repair; IMP:MGI.
DR GO; GO:0007005; P:mitochondrion organization; IMP:BHF-UCL.
DR GO; GO:0045910; P:negative regulation of DNA recombination; IMP:MGI.
DR GO; GO:0090298; P:negative regulation of mitochondrial DNA replication; ISO:MGI.
DR Gene3D; 1.10.3260.10; -; 1.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.30.1740.10; -; 1.
DR Gene3D; 3.40.50.10190; -; 1.
DR InterPro; IPR001357; BRCT_dom.
DR InterPro; IPR036420; BRCT_dom_sf.
DR InterPro; IPR000977; DNA_ligase_ATP-dep.
DR InterPro; IPR012309; DNA_ligase_ATP-dep_C.
DR InterPro; IPR012310; DNA_ligase_ATP-dep_cent.
DR InterPro; IPR016059; DNA_ligase_ATP-dep_CS.
DR InterPro; IPR012308; DNA_ligase_ATP-dep_N.
DR InterPro; IPR036599; DNA_ligase_N_sf.
DR InterPro; IPR031916; LIG3_BRCT.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR001510; Znf_PARP.
DR InterPro; IPR036957; Znf_PARP_sf.
DR Pfam; PF04679; DNA_ligase_A_C; 1.
DR Pfam; PF01068; DNA_ligase_A_M; 1.
DR Pfam; PF04675; DNA_ligase_A_N; 1.
DR Pfam; PF16759; LIG3_BRCT; 1.
DR Pfam; PF00645; zf-PARP; 1.
DR SMART; SM00292; BRCT; 1.
DR SMART; SM01336; zf-PARP; 1.
DR SUPFAM; SSF117018; SSF117018; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF52113; SSF52113; 1.
DR TIGRFAMs; TIGR00574; dnl1; 1.
DR PROSITE; PS50172; BRCT; 1.
DR PROSITE; PS00697; DNA_LIGASE_A1; 1.
DR PROSITE; PS00333; DNA_LIGASE_A2; 1.
DR PROSITE; PS50160; DNA_LIGASE_A3; 1.
DR PROSITE; PS00347; PARP_ZN_FINGER_1; 1.
DR PROSITE; PS50064; PARP_ZN_FINGER_2; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; ATP-binding; Cell cycle; Cell division; DNA damage;
KW DNA recombination; DNA repair; DNA replication; Ligase; Magnesium;
KW Metal-binding; Nucleotide-binding; Nucleus; Phosphoprotein;
KW Reference proteome; Zinc; Zinc-finger.
FT CHAIN 1..1015
FT /note="DNA ligase 3"
FT /id="PRO_0000059575"
FT DOMAIN 939..1015
FT /note="BRCT"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00033"
FT ZN_FING 94..186
FT /note="PARP-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00264"
FT REGION 229..255
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 279..282
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P49916"
FT REGION 323..328
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P49916"
FT REGION 393..396
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P49916"
FT REGION 426..432
FT /note="Interaction with DNA"
FT /evidence="ECO:0000250|UniProtKB:P49916"
FT REGION 849..926
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 229..251
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 878..895
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 513
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000250|UniProtKB:P49916,
FT ECO:0000255|PROSITE-ProRule:PRU10135"
FT BINDING 511
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P49916"
FT BINDING 518
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P49916"
FT BINDING 533
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 565
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000250"
FT BINDING 660
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000250"
FT BINDING 665
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:P49916"
FT BINDING 676
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 680
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT MOD_RES 211
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:17242355,
FT ECO:0007744|PubMed:19144319, ECO:0007744|PubMed:21183079"
FT MOD_RES 217
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P49916"
FT MOD_RES 228
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P49916"
FT MOD_RES 244
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P49916"
FT MOD_RES 919
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:P49916"
FT VAR_SEQ 939..1015
FT /note="VLLDVFTGVRLYLPPSTPDFKRLKRYFVAFDGDLVQEFDMGSATHVLGNREK
FT NTDAQLVSSEWIWACIRKRRLIAPC -> RRRASRQRGRKAMQTGRR (in isoform
FT Beta)"
FT /evidence="ECO:0000303|PubMed:9001252"
FT /id="VSP_001303"
FT CONFLICT 299..301
FT /note="GFS -> STG (in Ref. 1; AAC53003/AAC53004)"
FT /evidence="ECO:0000305"
FT CONFLICT 417
FT /note="Missing (in Ref. 1; AAC53003/AAC53004)"
FT /evidence="ECO:0000305"
FT CONFLICT 595
FT /note="V -> L (in Ref. 1; AAC53003/AAC53004)"
FT /evidence="ECO:0000305"
FT CONFLICT 702..705
FT /note="AFYG -> VFLI (in Ref. 1; AAC53003/AAC53004)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 1015 AA; 113072 MW; 9CBA3A100C968E77 CRC64;
MTLAFKILFP RNLCALGRKE LCLFPEQNRW AAISQFSQWS ETNLLGGCCL LQRRKPVLAL
QRGHLRPRAT HLTFWPGSHV GLCTGPCAMA EQRFCVDYAK RGTAGCKKCK EKIVKGVCRI
GKVVPNPFSE SGGDMKEWYH IKCMFEKLER ARATTKKIED LTELEGWEEL EDNEKEQISQ
HIADLSSKAA ATPKKKAAVQ AKLTTTGQVT SPVKGASFIT STNPRKFSGF SAAKPNNSEQ
APSSPAPGTS LSASKCDPKH KDCLLREFRK LCAMVAENPS YNTKTQIIHD FLQKGSTGGF
SDGFHGDVYL TVKLLLPGVI KSVYNLNDKQ IVKLFSRIFN CNPDDMARDL EQGDVSETIR
IFFEQSKSFP PAAKSLLTIQ EVDAFLLHLS KLTKEDEQQQ ALQDIASRCT ANDLKCIIRL
IKHDLKMNSG AKHVLDALDP NAYEAFKASR NLQDVVERVL HNEQEVEKDP GRRRALRVQA
SLMTPVQPML AEACKSIEYA MKKCPNGMFS EIKYDGERVQ VHKKGDHFSY FSRSLKPVLP
HKVAHFKDYI PKAFPGGQSM ILDSEVLLID NNTGKPLPFG TLGVHKKAAF QDANVCLFVF
DCIYFNDVSL MDRPLCERRK FLHDNMVEIR NRIMFSEMKQ VTKASDLADM INRVIREGLE
GLVLKDVKGT YEPGKRHWLK VKKDYLNEGA MADTADLVVL GAFYGQGSKG GMMSIFLMGC
YDPDSQKWCT VTKCAGGHDD ATLARLQKEL VMVKISKDPS KIPSWLKINK IYYPDFIVPD
PKKAAVWEIT GAEFSRSEAH TADGISIRFP RCTRIRDDKD WKSATNLPQL KELYQLSKDK
ADFAVVAGDE ASPTTGGSSG ENEGTAGSAG PCKGPPSKSS ASAKTTEQKL NSPSSRGGIK
PIPKHSPMKP GEKLAVKSSP VKVGMKRKAT DETPCLKKVL LDVFTGVRLY LPPSTPDFKR
LKRYFVAFDG DLVQEFDMGS ATHVLGNREK NTDAQLVSSE WIWACIRKRR LIAPC
