ID   DNLI3_DICDI             Reviewed;        1175 AA.
AC   Q54QM4;
DT   23-SEP-2008, integrated into UniProtKB/Swiss-Prot.
DT   24-MAY-2005, sequence version 1.
DT   27-MAR-2024, entry version 113.
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; ORFNames=DDB_G0283857;
OS   Dictyostelium discoideum (Social amoeba).
OC   Eukaryota; Amoebozoa; Evosea; Eumycetozoa; Dictyostelia; Dictyosteliales;
OC   Dictyosteliaceae; Dictyostelium.
OX   NCBI_TaxID=44689;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=AX4;
RX   PubMed=15875012; DOI=10.1038/nature03481;
RA   Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R.,
RA   Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B.,
RA   Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T.,
RA   Lehmann R., Hamlin N., Davies R., Gaudet P., Fey P., Pilcher K., Chen G.,
RA   Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N.,
RA   Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E.,
RA   Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N.,
RA   Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D.,
RA   Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T.,
RA   Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D.,
RA   Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A.,
RA   Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M.,
RA   Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A.,
RA   Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y.,
RA   Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C.,
RA   Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R.,
RA   Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A.;
RT   "The genome of the social amoeba Dictyostelium discoideum.";
RL   Nature 435:43-57(2005).
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   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC   -!- SIMILARITY: Belongs to the ATP-dependent DNA ligase family.
CC       {ECO:0000305}.
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DR   EMBL; AAFI02000057; EAL65543.1; -; Genomic_DNA.
DR   RefSeq; XP_638847.1; XM_633755.1.
DR   AlphaFoldDB; Q54QM4; -.
DR   SMR; Q54QM4; -.
DR   STRING; 44689.Q54QM4; -.
DR   PaxDb; 44689-DDB0232266; -.
DR   EnsemblProtists; EAL65543; EAL65543; DDB_G0283857.
DR   GeneID; 8624245; -.
DR   KEGG; ddi:DDB_G0283857; -.
DR   dictyBase; DDB_G0283857; lig3.
DR   eggNOG; KOG4437; Eukaryota.
DR   HOGENOM; CLU_273687_0_0_1; -.
DR   InParanoid; Q54QM4; -.
DR   OMA; GCRHWIK; -.
DR   PhylomeDB; Q54QM4; -.
DR   Reactome; R-DDI-110381; Resolution of AP sites via the single-nucleotide replacement pathway.
DR   Reactome; R-DDI-5649702; APEX1-Independent Resolution of AP Sites via the Single Nucleotide Replacement Pathway.
DR   PRO; PR:Q54QM4; -.
DR   Proteomes; UP000002195; Chromosome 4.
DR   GO; GO:0005634; C:nucleus; IBA:GO_Central.
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; IBA:GO_Central.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
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; IBA:GO_Central.
DR   GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR   GO; GO:0006281; P:DNA repair; IEA:UniProtKB-KW.
DR   GO; GO:0006273; P:lagging strand elongation; IBA:GO_Central.
DR   CDD; cd07902; Adenylation_DNA_ligase_III; 1.
DR   CDD; cd00027; BRCT; 1.
DR   CDD; cd07967; OBF_DNA_ligase_III; 1.
DR   Gene3D; 3.30.1490.70; -; 1.
DR   Gene3D; 3.40.50.10190; BRCT domain; 2.
DR   Gene3D; 1.10.3260.10; DNA ligase, ATP-dependent, N-terminal domain; 1.
DR   Gene3D; 3.30.470.30; DNA ligase/mRNA capping enzyme; 1.
DR   Gene3D; 3.40.220.10; Leucine Aminopeptidase, subunit E, domain 1; 1.
DR   Gene3D; 2.40.50.140; Nucleic acid-binding proteins; 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; IPR043472; Macro_dom-like.
DR   InterPro; IPR012340; NA-bd_OB-fold.
DR   NCBIfam; TIGR00574; dnl1; 1.
DR   PANTHER; PTHR45674; DNA LIGASE 1/3 FAMILY MEMBER; 1.
DR   PANTHER; PTHR45674:SF9; DNA LIGASE 3; 1.
DR   Pfam; PF00533; BRCT; 1.
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   SMART; SM00292; BRCT; 2.
DR   SUPFAM; SSF117018; ATP-dependent DNA ligase DNA-binding domain; 1.
DR   SUPFAM; SSF52113; BRCT domain; 2.
DR   SUPFAM; SSF56091; DNA ligase/mRNA capping enzyme, catalytic domain; 1.
DR   SUPFAM; SSF52949; Macro domain-like; 1.
DR   SUPFAM; SSF50249; Nucleic acid-binding proteins; 1.
DR   PROSITE; PS50172; BRCT; 2.
DR   PROSITE; PS00697; DNA_LIGASE_A1; 1.
DR   PROSITE; PS00333; DNA_LIGASE_A2; 1.
DR   PROSITE; PS50160; DNA_LIGASE_A3; 1.
PE   3: Inferred from homology;
KW   ATP-binding; Cell cycle; Cell division; DNA damage; DNA recombination;
KW   DNA repair; DNA replication; Ligase; Magnesium; Metal-binding;
KW   Nucleotide-binding; Nucleus; Reference proteome; Repeat.
FT   CHAIN           1..1175
FT                   /note="DNA ligase 3"
FT                   /id="PRO_0000351215"
FT   DOMAIN          883..976
FT                   /note="BRCT 1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00033"
FT   DOMAIN          1067..1174
FT                   /note="BRCT 2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00033"
FT   REGION          195..243
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          612..669
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          829..869
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   REGION          984..1036
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        201..219
FT                   /note="Acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        616..641
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        642..661
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        829..863
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        984..1014
FT                   /note="Polar residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   COMPBIAS        1015..1032
FT                   /note="Basic and acidic residues"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        283
FT                   /note="N6-AMP-lysine intermediate"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU10135"
FT   BINDING         281
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   BINDING         288
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   BINDING         303
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   BINDING         334
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255"
FT   BINDING         432
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255"
FT   BINDING         437
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   BINDING         448
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
FT   BINDING         452
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   1175 AA;  132048 MW;  D963D7D6EF49547E CRC64;
     MSEDKSGSFY SMYKLCGQLE KESSHSGKTQ LIKSFCNVFK GDLYLLAKLM LCKEDKRVFR
     IKDKAMLKIC SHIWDCDLDD MIEDLDNGDF TETCKKFYIE YGKYPEKSTL TLKEVDQVLD
     SLTVSGKFED QVKIINKLLK RCTPFDFRLV CRIIDSDLKI NTGAKFFLDA FHPQAYDAFK
     KANNLKGVIE KIQQHDFDND NGDGDDGDGD DNDDDDGDGD SDSDKKKKKS SGGSGSDSGS
     KKKSKSFEVA IKLMTPIKPM LPKAVKTVEG VVKSSECFYA EIKYDGERIQ IHKDGNQFSC
     YSRNLKPLMP WKVDEVKPYI PKSTKAQQMI LDGEILLMDT KTSQPLPFGT LSAHKKNGFK
     DATVCVFLFD ILYLNGKSLI HLPLKERREI LEKNVMVVKN RIEFSEVTIV NGASEKSKLT
     ALLNRVFKEK LEGLVIKDAM SEYEPGCRHW IKIKKDYIHG MADSADLIAV GGYYGSGSMG
     GLVTVFLMVC YDKQNKIYKT VVKASGGLDD NMIAKLQPKV TSTMTKISKE VSKIPYWLDC
     PKQYAPDFIV KDIKQAMIFE IESAEFTKSD HHTTGYSMRF PRILKIRHDK DYKTATTLEE
     LVEIGKDIKI VPVGKGDNNS PTTTTTTTTT TTTTTSSKLI KKQQLSDDDD DNDKDSKQQQ
     QEPSKLKFVS DDLLDPFNDK SDDESNKIFI LNYVDNSGIW NEKGLSGAIG KKWPSIPKSF
     SQGDSNIIKS GEIRVEKVKD DSISTNKKVF ICNLSCIIPP KSKKESYTFS LKEFKSAIKE
     AKGAINQKKA SVHLAKPQFT SPSWSELDEV LTKELYNSGI KVFVHSISKS SPTTTSPTTT
     SPTTTSPKIT SPSSSSSPSN KLSPLKRGRD EKLEHEIIKD IEPSLPIFED VNAVIDSKTI
     DQVDVKRLIN SIKTMGGRVS DKWQQVGIGK TTHLICNGMS DLYLHVDRLG GTIVLPNWVD
     QCFGSDKLLP LHEDYIYFNK KDHPDYSQSS SSSSMSIEEE KIVVTTTSDD PSEGNQQQQD
     KKVIKESKII QSKDHSSTTT IDTKITITST NNNNNGNDNN KTRKKQHLLS IFQECIIFLH
     DNVNDRETLK RYIIAYGGDI SDSVNDKTTH LVASLPNNFS NVKPKDLFKS IINNNSKNNN
     NNNNNNNNGI IVNSLWLWDS INMSDLLDVK NYKLF
//