DNLI4_ARATH
ID DNLI4_ARATH Reviewed; 1219 AA.
AC Q9LL84; Q9LU70;
DT 24-JAN-2006, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 148.
DE RecName: Full=DNA ligase 4;
DE EC=6.5.1.1 {ECO:0000255|PROSITE-ProRule:PRU10135};
DE AltName: Full=DNA ligase IV;
DE AltName: Full=Polydeoxyribonucleotide synthase [ATP] 4;
GN Name=LIG4; OrderedLocusNames=At5g57160; ORFNames=MUL3.11;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], INDUCTION, TISSUE SPECIFICITY, AND INTERACTION
RP WITH XRCC4.
RX PubMed=11029705; DOI=10.1046/j.1365-313x.2000.00856.x;
RA West C.E., Waterworth W.M., Jiang Q., Bray C.M.;
RT "Arabidopsis DNA ligase IV is induced by gamma-irradiation and interacts
RT with an Arabidopsis homologue of the double strand break repair protein
RT XRCC4.";
RL Plant J. 24:67-78(2000).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=10718197; DOI=10.1093/dnares/7.1.31;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Kotani H.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence
RT features of the regions of 3,076,755 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:31-63(2000).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP FUNCTION.
RX PubMed=12853643; DOI=10.1093/nar/gkg458;
RA van Attikum H., Bundock P., Overmeer R.M., Lee L.-Y., Gelvin S.B.,
RA Hooykaas P.J.J.;
RT "The Arabidopsis AtLIG4 gene is required for the repair of DNA damage, but
RT not for the integration of Agrobacterium T-DNA.";
RL Nucleic Acids Res. 31:4247-4255(2003).
RN [5]
RP INDUCTION.
RX PubMed=12509526; DOI=10.1105/tpc.006577;
RA Garcia V., Bruchet H., Camescasse D., Granier F., Bouchez D., Tissier A.;
RT "AtATM is essential for meiosis and the somatic response to DNA damage in
RT plants.";
RL Plant Cell 15:119-132(2003).
RN [6]
RP FUNCTION.
RX PubMed=12753583; DOI=10.1046/j.1365-313x.2003.01738.x;
RA Friesner J., Britt A.B.;
RT "Ku80- and DNA ligase IV-deficient plants are sensitive to ionizing
RT radiation and defective in T-DNA integration.";
RL Plant J. 34:427-440(2003).
RN [7]
RP INTERACTION WITH POLL.
RX PubMed=23660835; DOI=10.1104/pp.113.219022;
RA Roy S., Choudhury S.R., Sengupta D.N., Das K.P.;
RT "Involvement of AtPollambda in the repair of high salt- and DNA cross-
RT linking agent-induced double strand breaks in Arabidopsis.";
RL Plant Physiol. 162:1195-1210(2013).
CC -!- FUNCTION: Efficiently joins single-strand breaks in a double-stranded
CC polydeoxynucleotide in an ATP-dependent reaction. Involved in DNA non-
CC homologous end joining (NHEJ) required for double-strand break repair.
CC May be involved for T-DNA integration even if not absolutely required.
CC Seems to be dispensable under normal growth conditions.
CC {ECO:0000269|PubMed:12753583, ECO:0000269|PubMed:12853643}.
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 with XRCC4 via its tandem BRCT domains
CC (PubMed:11029705). Interacts with POLL (PubMed:23660835).
CC {ECO:0000269|PubMed:11029705, ECO:0000269|PubMed:23660835}.
CC -!- INTERACTION:
CC Q9LL84; Q682V0: XRCC4; NbExp=2; IntAct=EBI-2127971, EBI-2128002;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250}.
CC -!- TISSUE SPECIFICITY: Widely expressed, with higher levels in young
CC flowers and roots. {ECO:0000269|PubMed:11029705}.
CC -!- INDUCTION: Induced by gamma radiation and by white light, but not by
CC UV-B. Regulated by ATM in response to DNA double strand breaks (DSBs).
CC {ECO:0000269|PubMed:11029705, ECO:0000269|PubMed:12509526}.
CC -!- SIMILARITY: Belongs to the ATP-dependent DNA ligase family.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA97366.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AF233527; AAF91284.1; -; mRNA.
DR EMBL; AB023042; BAA97366.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED96857.1; -; Genomic_DNA.
DR RefSeq; NP_568851.2; NM_125098.4.
DR AlphaFoldDB; Q9LL84; -.
DR SMR; Q9LL84; -.
DR BioGRID; 21066; 3.
DR IntAct; Q9LL84; 1.
DR STRING; 3702.AT5G57160.1; -.
DR iPTMnet; Q9LL84; -.
DR PaxDb; Q9LL84; -.
DR PRIDE; Q9LL84; -.
DR ProteomicsDB; 222612; -.
DR EnsemblPlants; AT5G57160.1; AT5G57160.1; AT5G57160.
DR GeneID; 835822; -.
DR Gramene; AT5G57160.1; AT5G57160.1; AT5G57160.
DR KEGG; ath:AT5G57160; -.
DR Araport; AT5G57160; -.
DR TAIR; locus:2175544; AT5G57160.
DR eggNOG; KOG0966; Eukaryota.
DR HOGENOM; CLU_004844_3_0_1; -.
DR InParanoid; Q9LL84; -.
DR OMA; EGIMIKH; -.
DR OrthoDB; 274264at2759; -.
DR PhylomeDB; Q9LL84; -.
DR PRO; PR:Q9LL84; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9LL84; baseline and differential.
DR Genevisible; Q9LL84; AT.
DR GO; GO:0032807; C:DNA ligase IV complex; IBA:GO_Central.
DR GO; GO:0009506; C:plasmodesma; HDA:TAIR.
DR GO; GO:0005524; F:ATP binding; IBA:GO_Central.
DR GO; GO:0003677; F:DNA binding; IBA:GO_Central.
DR GO; GO:0003910; F:DNA ligase (ATP) activity; IDA:TAIR.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006974; P:cellular response to DNA damage stimulus; IMP:TAIR.
DR GO; GO:0071897; P:DNA biosynthetic process; IEA:InterPro.
DR GO; GO:0051103; P:DNA ligation involved in DNA repair; IEA:InterPro.
DR GO; GO:0006310; P:DNA recombination; IEA:UniProtKB-KW.
DR GO; GO:0006260; P:DNA replication; IEA:UniProtKB-KW.
DR GO; GO:0006302; P:double-strand break repair; IMP:TAIR.
DR GO; GO:0006303; P:double-strand break repair via nonhomologous end joining; IMP:TAIR.
DR GO; GO:0006297; P:nucleotide-excision repair, DNA gap filling; IBA:GO_Central.
DR GO; GO:0010165; P:response to X-ray; IMP:TAIR.
DR CDD; cd07903; Adenylation_DNA_ligase_IV; 1.
DR Gene3D; 1.10.3260.10; -; 1.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.40.50.10190; -; 2.
DR InterPro; IPR044125; Adenylation_DNA_ligase_IV.
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; IPR029710; LIG4.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR PANTHER; PTHR45997; PTHR45997; 1.
DR Pfam; PF16589; BRCT_2; 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 SMART; SM00292; BRCT; 1.
DR SUPFAM; SSF117018; SSF117018; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF52113; SSF52113; 2.
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 1: Evidence at protein level;
KW ATP-binding; DNA damage; DNA recombination; DNA repair; DNA replication;
KW Ligase; Magnesium; Metal-binding; Nucleotide-binding; Nucleus;
KW Reference proteome; Repeat.
FT CHAIN 1..1219
FT /note="DNA ligase 4"
FT /id="PRO_0000059580"
FT DOMAIN 651..739
FT /note="BRCT 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00033"
FT DOMAIN 807..909
FT /note="BRCT 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00033"
FT REGION 604..632
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 914..1126
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1146..1197
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 614..631
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 914..930
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 931..977
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 982..1014
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1080..1098
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1147..1163
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1168..1183
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 253
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10135"
FT BINDING 251
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 258
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 273
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 303
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255"
FT BINDING 418
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255"
FT BINDING 423
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 434
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 440
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1219 AA; 137851 MW; 97825B4B795E45FB CRC64;
MTEEIKFSVL VSLFNWIQKS KTSSQKRSKF RKFLDTYCKP SDYFVAVRLI IPSLDRERGS
YGLKESVLAT CLIDALGISR DAPDAVRLLN WRKGGTAKAG ANAGNFSLIA AEVLQRRQGM
ASGGLTIKEL NDLLDRLASS ENRAEKTLVL STLIQKTNAQ EMKWVIRIIL KDLKLGMSEK
SIFQEFHPDA EDLFNVTCDL KLVCEKLRDR HQRHKRQDIE VGKAVRPQLA MRIGDVNAAW
KKLHGKDVVA ECKFDGDRIQ IHKNGTDIHY FSRNFLDHSE YAHAMSDLIV QNILVDKCIL
DGEMLVWDTS LNRFAEFGSN QEIAKAAREG LDSHKQLCYV AFDVLYVGDT SVIHQSLKER
HELLKKVVKP LKGRLEVLVP EGGLNVHRPS GEPSWSIVVH AAADVERFFK ETVENRDEGI
VLKDLESKWE PGDRSGKWMK LKPEYIRAGA DLDVLIIGGY YGSGRRGGEV AQFLVALADR
AEANVYPRRF MSFCRVGTGL SDDELNTVVS KLKPYFRKNE HPKKAPPSFY QVTNHSKERP
DVWIDSPEKS IILSITSDIR TIRSEVFVAP YSLRFPRIDK VRYDKPWHEC LDVQAFVELV
NSSNGTTQKQ KESESTQDNP KVNKSSKRGE KKNVSLVPSQ FIQTDVSDIK GKTSIFSNMI
FYFVNVPRSH SLETFHKMVV ENGGKFSMNL NNSVTHCIAA ESSGIKYQAA KRQRDVIHFS
WVLDCCSRNK MLPLLPKYFL HLTDASRTKL QDDIDEFSDS YYWDLDLEGL KQVLSNAKQS
EDSKSIDYYK KKLCPEKRWS CLLSCCVYFY PYSQTLSTEE EALLGIMAKR LMLEVLMAGG
KVSNNLAHAS HLVVLAMAEE PLDFTLVSKS FSEMEKRLLL KKRLHVVSSH WLEESLQREE
KLCEDVYTLR PKYMEESDTE ESDKSEHDTT EVASQGSAQT KEPASSKIAI TSSRGRSNTR
AVKRGRSSTN SLQRVQRRRG KQPSKISGDE TEESDASEEK VSTRLSDIAE ETDSFGEAQR
NSSRGKCAKR GKSRVGQTQR VQRSRRGKKA AKIGGDESDE NDELDGNNNV SADAEEGNAA
GRSVENEETR EPDIAKYTES QQRDNTVAVE EALQDSRNAK TEMDMKEKLQ IHEDPLQAML
MKMFPIPSQK TTETSNRTTG EYRKANVSGE CESSEKRKLD AETDNTSVNA GAESDVVPPL
VKKKKVSYRD VAGELLKDW
