DNLI4_ORYSJ
ID DNLI4_ORYSJ Reviewed; 1322 AA.
AC Q7X7E9;
DT 25-JUL-2006, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 2.
DT 03-AUG-2022, entry version 88.
DE RecName: Full=Putative 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=Os04g0606450, LOC_Os04g51700;
GN ORFNames=OSJNBa0035M09.8;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12447439; DOI=10.1038/nature01183;
RA Feng Q., Zhang Y., Hao P., Wang S., Fu G., Huang Y., Li Y., Zhu J., Liu Y.,
RA Hu X., Jia P., Zhang Y., Zhao Q., Ying K., Yu S., Tang Y., Weng Q.,
RA Zhang L., Lu Y., Mu J., Lu Y., Zhang L.S., Yu Z., Fan D., Liu X., Lu T.,
RA Li C., Wu Y., Sun T., Lei H., Li T., Hu H., Guan J., Wu M., Zhang R.,
RA Zhou B., Chen Z., Chen L., Jin Z., Wang R., Yin H., Cai Z., Ren S., Lv G.,
RA Gu W., Zhu G., Tu Y., Jia J., Zhang Y., Chen J., Kang H., Chen X., Shao C.,
RA Sun Y., Hu Q., Zhang X., Zhang W., Wang L., Ding C., Sheng H., Gu J.,
RA Chen S., Ni L., Zhu F., Chen W., Lan L., Lai Y., Cheng Z., Gu M., Jiang J.,
RA Li J., Hong G., Xue Y., Han B.;
RT "Sequence and analysis of rice chromosome 4.";
RL Nature 420:316-320(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1068-1322.
RC STRAIN=cv. Nipponbare;
RG The rice full-length cDNA consortium;
RT "Oryza sativa full length cDNA.";
RL Submitted (OCT-2006) to the EMBL/GenBank/DDBJ databases.
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; AL662968; CAD41778.2; -; Genomic_DNA.
DR EMBL; AP014960; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AK242148; -; NOT_ANNOTATED_CDS; mRNA.
DR AlphaFoldDB; Q7X7E9; -.
DR SMR; Q7X7E9; -.
DR STRING; 4530.OS04T0606450-01; -.
DR PRIDE; Q7X7E9; -.
DR eggNOG; KOG0966; Eukaryota.
DR InParanoid; Q7X7E9; -.
DR Proteomes; UP000000763; Chromosome 4.
DR Proteomes; UP000059680; Chromosome 4.
DR Genevisible; Q7X7E9; OS.
DR GO; GO:0032807; C:DNA ligase IV complex; IBA:GO_Central.
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; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
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:0006303; P:double-strand break repair via nonhomologous end joining; IBA:GO_Central.
DR GO; GO:0006297; P:nucleotide-excision repair, DNA gap filling; IBA:GO_Central.
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; 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; IPR021536; DNA_ligase_IV_dom.
DR InterPro; IPR036599; DNA_ligase_N_sf.
DR InterPro; IPR029710; LIG4.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR PANTHER; PTHR45997; PTHR45997; 2.
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 Pfam; PF11411; DNA_ligase_IV; 1.
DR SUPFAM; SSF117018; SSF117018; 1.
DR SUPFAM; SSF50249; SSF50249; 1.
DR SUPFAM; SSF52113; SSF52113; 2.
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 2: Evidence at transcript 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..1322
FT /note="Putative DNA ligase 4"
FT /id="PRO_0000247468"
FT DOMAIN 686..768
FT /note="BRCT 1"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00033"
FT DOMAIN 825..935
FT /note="BRCT 2"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00033"
FT REGION 945..1212
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1245..1310
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 945..970
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1004..1052
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1062..1108
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1121..1161
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1176..1193
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1253..1296
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 267
FT /note="N6-AMP-lysine intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10135"
FT BINDING 265
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 272
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 287
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 317
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255"
FT BINDING 497
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255"
FT BINDING 502
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 513
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
FT BINDING 519
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250"
SQ SEQUENCE 1322 AA; 149078 MW; 110BF7B94DB62A67 CRC64;
MAATVRFGLL VAMFQAMSRD RTAAKKRARL RALLDRAYGP GGRDDYFSAL RLVLPGLDRE
RGSYGLKEAA LASVLVDALG IAKDSPDAVR LTNWRRGGGF RNAGNFALVA AEVLQRRQGM
TSGGLTIKEV NDALDRLAAT ENSVCLESEK LLLILDRSEK ASILSSLIKK TNALEMKWLL
MIILKDLKLG ISEKSVFHEF HPDAEDLFNV TCDLRLVCEK LNDRSQRHKR QDIEVGKAVR
PQLSMRVNNA SSAWKKLHGK QVVAECKFDG DRIQIHKNGE EIHFFSRSFL DHSEYAPGMS
KVIIENILVD RCILDGEMLV WDTVLNRFAE FGSNQEIAKA AKEGLETDRQ LCCILEWIAS
YVLALCVNIL SCQDFFFSNK RESYVAFDIL YAGDTSVIHQ SLTERHEILQ KVVRPLKGHL
EILVPTGGLN IHRPPDEPCW SILAHSLDDV EKFFKDTVDN RFFPTSPNTD ELSNLSISLM
IQFRFSDYSI CYVLREEGII LKDLESKWEP GDRSGKWLKL KPDYIHAGAD LDVIIIGGYY
GSGRRGGEVA QFLVGLAVPS DDNSYPKRFL SFCRVGTGLS DEELDALVTK LKPHFRKNEY
PKKPPRFYEV TNHSKERPDV WIESPDKQSV RFRKHLIYCI TKCRSVIISI TSDIRTIKSE
VFAAPYSLRF PRIQRLRYDK PWHECLDVQA FVDIVHSSNG TTHRAADDDN DLKNVKNGGS
FSMNLNDSVT HCIAAEKKAT RQGRIIHYSW ILDCCKEKRL LHLQPKFDPC LQPMHKFPEE
IDSYADYFYW DIDISDLKQI FSNMDRAVVD SNMVHHYKKK YCADERFCFF QGCCVYFYHA
PLVNADYNVI SDLALKRVKQ DLTMHGGQVC SILAPATHLI IVSVLQAYNF DMLYKSLPPA
ERRYLHDKRL QVVSNKWLED SVEKQTRLPE TTYSLKPDTL EEIEIERSEE TVQPCNDKLE
ENEKADTSHV KHAPRKRGRP SSSASRTAKP APRPVRRTRA RRGNQHAKID DVEPEESDHG
ETGLDDQIPD TDNISKMEVD SFDKDQVSAR PVRRTRARRG KQHAKIDYGQ SEESDPGETG
QDDQRLDADY ISKMEEDSSD RDQGAHPTAP RVVRRSRAQR GKWLAKIDRE TGPGETGQDD
KKLNADSISK MEEHAHDKDQ EPPPGAQLIT LDEQEPKGIK SSTTETPSSP KHERNQTVLR
RDTAETTSSA TCEKMEQMVD PLHAMLLDMI PSLGQMKTDV GNRVAEAKAE TNPPWVGSST
SSYVAPVPQA SASSASSSGV PAPHAGSSTQ STGVPAPDPT AGAPKKKKVS YKDVAGALLK
DW
