DNLI3_DICDI
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 03-AUG-2022, entry version 105.
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 (Slime mold).
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.DDB0232266; -.
DR PaxDb; Q54QM4; -.
DR PRIDE; Q54QM4; -.
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; SMRFPRI; -.
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:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0070421; C:DNA ligase III-XRCC1 complex; IBA:GO_Central.
DR GO; GO:0005739; C:mitochondrion; IEA:GOC.
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:0006288; P:base-excision repair, DNA ligation; IBA:GO_Central.
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:0097681; P:double-strand break repair via alternative nonhomologous end joining; IBA:GO_Central.
DR GO; GO:0006273; P:lagging strand elongation; IBA:GO_Central.
DR GO; GO:0043504; P:mitochondrial DNA repair; IBA:GO_Central.
DR Gene3D; 1.10.3260.10; -; 1.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.40.220.10; -; 1.
DR Gene3D; 3.40.50.10190; -; 2.
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 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; SSF117018; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF52113; SSF52113; 2.
DR SUPFAM; SSF52949; SSF52949; 1.
DR TIGRFAMs; TIGR00574; dnl1; 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
