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Database: UniProt/SWISS-PROT
Entry: DNLI4_ARATH
LinkDB: DNLI4_ARATH
Original site: 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   27-SEP-2017, entry version 123.
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; Magnoliophyta; eudicotyledons; Gunneridae;
OC   Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
OC   Arabidopsis.
OX   NCBI_TaxID=3702;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA], INDUCTION, TISSUE SPECIFICITY, AND
RP   INTERACTION 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
RT   interacts with an Arabidopsis homologue of the double strand break
RT   repair protein 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;
RG   The Arabidopsis Information Portal (Araport);
RL   Submitted (MAY-2016) to the EMBL/GenBank/DDBJ databases.
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,
RT   but 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.,
RA   Tissier A.;
RT   "AtATM is essential for meiosis and the somatic response to DNA damage
RT   in 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-
CC       stranded polydeoxynucleotide in an ATP-dependent reaction.
CC       Involved in DNA non-homologous end joining (NHEJ) required for
CC       double-strand break repair. May be involved for T-DNA integration
CC       even if not absolutely required. Seems to be dispensable under
CC       normal growth conditions. {ECO:0000269|PubMed:12753583,
CC       ECO:0000269|PubMed:12853643}.
CC   -!- CATALYTIC ACTIVITY: ATP + (deoxyribonucleotide)(n)-3'-hydroxyl +
CC       5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) +
CC       AMP + diphosphate. {ECO:0000255|PROSITE-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       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
CC       by UV-B. Regulated by ATM in response to DNA double strand breaks
CC       (DSBs). {ECO:0000269|PubMed:11029705,
CC       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};
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   UniGene; At.49182; -.
DR   UniGene; At.69713; -.
DR   ProteinModelPortal; Q9LL84; -.
DR   SMR; Q9LL84; -.
DR   BioGrid; 21066; 3.
DR   IntAct; Q9LL84; 1.
DR   MINT; MINT-8071190; -.
DR   STRING; 3702.AT5G57160.1; -.
DR   iPTMnet; Q9LL84; -.
DR   PaxDb; Q9LL84; -.
DR   PRIDE; Q9LL84; -.
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   eggNOG; COG1793; LUCA.
DR   HOGENOM; HOG000083793; -.
DR   InParanoid; Q9LL84; -.
DR   KO; K10777; -.
DR   OMA; HMCPSTK; -.
DR   OrthoDB; EOG093600VG; -.
DR   PhylomeDB; Q9LL84; -.
DR   PRO; PR:Q9LL84; -.
DR   Proteomes; UP000006548; Chromosome 5.
DR   Genevisible; Q9LL84; AT.
DR   GO; GO:0048046; C:apoplast; IDA:TAIR.
DR   GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR   GO; GO:0032807; C:DNA ligase IV complex; IBA:GO_Central.
DR   GO; GO:0009506; C:plasmodesma; IDA:TAIR.
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; 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; IBA:GO_Central.
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; cd00027; BRCT; 1.
DR   Gene3D; 1.10.3260.10; -; 1.
DR   Gene3D; 3.40.50.10190; -; 2.
DR   InterPro; IPR001357; BRCT_dom.
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; IPR029710; LIG4.
DR   InterPro; IPR012340; NA-bd_OB-fold.
DR   PANTHER; PTHR10459:SF84; PTHR10459:SF84; 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; Complete proteome; DNA damage; DNA recombination;
KW   DNA repair; DNA replication; Ligase; Magnesium; Metal-binding;
KW   Nucleotide-binding; Nucleus; Reference proteome; Repeat.
FT   CHAIN         1   1219       DNA ligase 4.
FT                                /FTId=PRO_0000059580.
FT   DOMAIN      651    739       BRCT 1. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00033}.
FT   DOMAIN      807    909       BRCT 2. {ECO:0000255|PROSITE-
FT                                ProRule:PRU00033}.
FT   ACT_SITE    253    253       N6-AMP-lysine intermediate.
FT                                {ECO:0000255|PROSITE-ProRule:PRU10135}.
FT   METAL       303    303       Magnesium 1. {ECO:0000255}.
FT   METAL       418    418       Magnesium 2. {ECO:0000255}.
FT   BINDING     251    251       ATP. {ECO:0000250}.
FT   BINDING     258    258       ATP. {ECO:0000250}.
FT   BINDING     273    273       ATP. {ECO:0000250}.
FT   BINDING     423    423       ATP. {ECO:0000250}.
FT   BINDING     434    434       ATP. {ECO:0000250}.
FT   BINDING     440    440       ATP. {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
//
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