Q42572 (DNLI1_ARATH) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
DNA ligase 1
Short name=AtLIG1
EC=6.5.1.1

Alternative name(s):
DNA ligase I
Polydeoxyribonucleotide synthase [ATP] 1

Gene names

Name:	LIG1
Ordered Locus Names:	At1g08130
ORF Names:	T23G18.1, T6D22.23

Organism

Arabidopsis thaliana (Mouse-ear cress) [Reference proteome]

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Viridiplantae › Streptophyta › Streptophytina › Embryophyta › Tracheophyta › Euphyllophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › malvids › Brassicales › Brassicaceae › Camelineae › Arabidopsis

Protein attributes

Sequence length	790 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at transcript level

General annotation (Comments)

Function	Essential protein. DNA ligase that seals nicks in double-stranded DNA during DNA replication, DNA recombination and DNA repair. Involved in repair of both single strand breaks (SSBs) and double strand breaks (DSBs). Required in the endosperm for embryogenesis, probably to repair DNA-breaks generated by DME. Ref.9 Ref.10
Catalytic activity	ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).
Cofactor	Magnesium By similarity.
Subcellular location	Isoform 1: Mitochondrion Ref.7 Ref.10. Isoform 2: Nucleus Ref.7 Ref.10. Isoform 3: Nucleus Ref.7 Ref.10.
Tissue specificity	Expressed in all vegetative and reproductive tissues. Ref.10
Developmental stage	In the mature male gametophyte, expressed in the vegetative cell as well as in the two sperm cells. In the mature female gametes, accumulates in the embryo sac; mostly expressed in the central cell nucleus and, at lower levels, in the egg cell and synergids. After fertilization, localized in the syncytial endosperm and in the embryo. Ref.10
Disruption phenotype	Lethal. Ref.9
Sequence similarities	Belongs to the ATP-dependent DNA ligase family.
Sequence caution	The sequence AAF18258.1 differs from that shown. Reason: Erroneous gene model prediction. The sequence AAF79833.1 differs from that shown. Reason: Erroneous gene model prediction. The sequence BAD95276.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.

Ontologies

Keywords
Biological process	Cell cycle Cell division DNA damage DNA recombination DNA repair DNA replication
Cellular component	Mitochondrion Nucleus
Coding sequence diversity	Alternative initiation
Domain	Repeat Transit peptide
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Ligase
Technical term	Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	DNA ligation involved in DNA repair Inferred from electronic annotation. Source: InterPro DNA recombination Inferred from electronic annotation. Source: UniProtKB-KW DNA replication Inferred from mutant phenotype Ref.9. Source: UniProtKB cell cycle Inferred from electronic annotation. Source: UniProtKB-KW cell division Inferred from electronic annotation. Source: UniProtKB-KW double-strand break repair Inferred from mutant phenotype Ref.9. Source: UniProtKB single strand break repair Inferred from mutant phenotype Ref.9. Source: UniProtKB
Cellular_component	mitochondrion Inferred from direct assay Ref.7. Source: TAIR nucleus Inferred from direct assay Ref.7. Source: TAIR
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA binding Inferred from electronic annotation. Source: InterPro DNA ligase (ATP) activity Inferred from Biological aspect of Ancestor. Source: RefGenome metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative initiation. [Align] [Select]

Isoform 1 (identifier: Q42572-1)

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

Isoform 2 (identifier: Q42572-2)

The sequence of this isoform differs from the canonical sequence as follows:
     1-47: Missing.

Isoform 3 (identifier: Q42572-3)

The sequence of this isoform differs from the canonical sequence as follows:
     1-59: Missing.

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Transit peptide	1 – 64	64	Mitochondrion Potential
	Chain	65 – 790	726	DNA ligase 1		PRO_0000059586
Regions
	Region	337 – 346	10	Interaction with target DNA By similarity
	Region	518 – 520	3	Interaction with target DNA By similarity
	Motif	68 – 75	8	Nuclear localization signal 1 By similarity
	Motif	505 – 512	8	Nuclear localization signal 2 By similarity
Sites
	Active site	444	1	N6-AMP-lysine intermediate By similarity
	Metal binding	497	1	Magnesium 1 By similarity
	Metal binding	596	1	Magnesium 2 By similarity
	Binding site	442	1	ATP By similarity
	Binding site	449	1	ATP By similarity
	Binding site	465	1	ATP By similarity
	Binding site	601	1	ATP By similarity
	Binding site	614	1	ATP By similarity
	Binding site	620	1	ATP By similarity
	Site	193	1	Interaction with target DNA By similarity
	Site	466	1	Interaction with target DNA By similarity
	Site	646	1	Interaction with target DNA By similarity
	Site	671	1	Interaction with target DNA By similarity
Natural variations
	Alternative sequence	1 – 59	59	Missing in isoform 3.		VSP_043693
	Alternative sequence	1 – 47	47	Missing in isoform 2.		VSP_043694
Experimental info
	Sequence conflict	639	1	A → P in CAA66599. Ref.1

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified January 10, 2003. Version 2. Checksum: 674EB9CAA9C5D329	FASTA	790	87,740
	10 20 30 40 50 60 MLAIRSSNYL RCIPSLCTKT QISQFSSVLI SFSRQISHLR LSSCHRAMSS SRPSAFDALM 70 80 90 100 110 120 SNARAAAKKK TPQTTNLSRS PNKRKIGETQ DANLGKTIVS EGTLPKTEDL LEPVSDSANP 130 140 150 160 170 180 RSDTSSIAED SKTGAKKAKT LSKTDEMKSK IGLLKKKPND FDPEKMSCWE KGERVPFLFV 190 200 210 220 230 240 ALAFDLISNE SGRIVITDIL CNMLRTVIAT TPEDLVATVY LSANEIAPAH EGVELGIGES 250 260 270 280 290 300 TIIKAISEAF GRTEDHVKKQ NTELGDLGLV AKGSRSTQTM MFKPEPLTVV KVFDTFRQIA 310 320 330 340 350 360 KESGKDSNEK KKNRMKALLV ATTDCEPLYL TRLLQAKLRL GFSGQTVLAA LGQAAVYNEE 370 380 390 400 410 420 HSKPPPNTKS PLEEAAKIVK QVFTVLPVYD IIVPALLSGG VWNLPKTCNF TLGVPIGPML 430 440 450 460 470 480 AKPTKGVAEI LNKFQDIVFT CEYKYDGERA QIHFMEDGTF EIYSRNAERN TGKYPDVALA 490 500 510 520 530 540 LSRLKKPSVK SFILDCEVVA FDREKKKILP FQILSTRARK NVNVNDIKVG VCIFAFDMLY 550 560 570 580 590 600 LNGQQLIQEN LKIRREKLYE SFEEDPGYFQ FATAVTSNDI DEIQKFLDAS VDVGCEGLII 610 620 630 640 650 660 KTLDSDATYE PAKRSNNWLK LKKDYMDSIG DSVDLVPIAA FHGRGKRTGV YGAFLLACYD 670 680 690 700 710 720 VDKEEFQSIC KIGTGFSDAM LDERSSSLRS QVIATPKQYY RVGDSLNPDV WFEPTEVWEV 730 740 750 760 770 780 KAADLTISPV HRAATGIVDP DKGISLRFPR LLRVREDKKP EEATSSEQIA DLYQAQKHNH 790 PSNEVKGDDD
	Isoform 2 [UniParc]. Checksum: D7DCE08F0DBC0C4D	FASTA	743	82,417
	10 20 30 40 50 60 MSSSRPSAFD ALMSNARAAA KKKTPQTTNL SRSPNKRKIG ETQDANLGKT IVSEGTLPKT 70 80 90 100 110 120 EDLLEPVSDS ANPRSDTSSI AEDSKTGAKK AKTLSKTDEM KSKIGLLKKK PNDFDPEKMS 130 140 150 160 170 180 CWEKGERVPF LFVALAFDLI SNESGRIVIT DILCNMLRTV IATTPEDLVA TVYLSANEIA 190 200 210 220 230 240 PAHEGVELGI GESTIIKAIS EAFGRTEDHV KKQNTELGDL GLVAKGSRST QTMMFKPEPL 250 260 270 280 290 300 TVVKVFDTFR QIAKESGKDS NEKKKNRMKA LLVATTDCEP LYLTRLLQAK LRLGFSGQTV 310 320 330 340 350 360 LAALGQAAVY NEEHSKPPPN TKSPLEEAAK IVKQVFTVLP VYDIIVPALL SGGVWNLPKT 370 380 390 400 410 420 CNFTLGVPIG PMLAKPTKGV AEILNKFQDI VFTCEYKYDG ERAQIHFMED GTFEIYSRNA 430 440 450 460 470 480 ERNTGKYPDV ALALSRLKKP SVKSFILDCE VVAFDREKKK ILPFQILSTR ARKNVNVNDI 490 500 510 520 530 540 KVGVCIFAFD MLYLNGQQLI QENLKIRREK LYESFEEDPG YFQFATAVTS NDIDEIQKFL 550 560 570 580 590 600 DASVDVGCEG LIIKTLDSDA TYEPAKRSNN WLKLKKDYMD SIGDSVDLVP IAAFHGRGKR 610 620 630 640 650 660 TGVYGAFLLA CYDVDKEEFQ SICKIGTGFS DAMLDERSSS LRSQVIATPK QYYRVGDSLN 670 680 690 700 710 720 PDVWFEPTEV WEVKAADLTI SPVHRAATGI VDPDKGISLR FPRLLRVRED KKPEEATSSE 730 740 QIADLYQAQK HNHPSNEVKG DDD
	Isoform 3 [UniParc]. Checksum: 72E76F2F2A57830B	FASTA	731	81,167
	10 20 30 40 50 60 MSNARAAAKK KTPQTTNLSR SPNKRKIGET QDANLGKTIV SEGTLPKTED LLEPVSDSAN 70 80 90 100 110 120 PRSDTSSIAE DSKTGAKKAK TLSKTDEMKS KIGLLKKKPN DFDPEKMSCW EKGERVPFLF 130 140 150 160 170 180 VALAFDLISN ESGRIVITDI LCNMLRTVIA TTPEDLVATV YLSANEIAPA HEGVELGIGE 190 200 210 220 230 240 STIIKAISEA FGRTEDHVKK QNTELGDLGL VAKGSRSTQT MMFKPEPLTV VKVFDTFRQI 250 260 270 280 290 300 AKESGKDSNE KKKNRMKALL VATTDCEPLY LTRLLQAKLR LGFSGQTVLA ALGQAAVYNE 310 320 330 340 350 360 EHSKPPPNTK SPLEEAAKIV KQVFTVLPVY DIIVPALLSG GVWNLPKTCN FTLGVPIGPM 370 380 390 400 410 420 LAKPTKGVAE ILNKFQDIVF TCEYKYDGER AQIHFMEDGT FEIYSRNAER NTGKYPDVAL 430 440 450 460 470 480 ALSRLKKPSV KSFILDCEVV AFDREKKKIL PFQILSTRAR KNVNVNDIKV GVCIFAFDML 490 500 510 520 530 540 YLNGQQLIQE NLKIRREKLY ESFEEDPGYF QFATAVTSND IDEIQKFLDA SVDVGCEGLI 550 560 570 580 590 600 IKTLDSDATY EPAKRSNNWL KLKKDYMDSI GDSVDLVPIA AFHGRGKRTG VYGAFLLACY 610 620 630 640 650 660 DVDKEEFQSI CKIGTGFSDA MLDERSSSLR SQVIATPKQY YRVGDSLNPD VWFEPTEVWE 670 680 690 700 710 720 VKAADLTISP VHRAATGIVD PDKGISLRFP RLLRVREDKK PEEATSSEQI ADLYQAQKHN 730 HPSNEVKGDD D

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Molecular cloning and functional analysis of the Arabidopsis thaliana DNA ligase I homologue." Taylor R.M., Hamer M.J., Rosamond J., Bray C.M. Plant J. 14:75-81(1998) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Strain: cv. Landsberg erecta.
[2]	"Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana." Theologis A., Ecker J.R., Palm C.J., Federspiel N.A., Kaul S., White O., Alonso J., Altafi H., Araujo R., Bowman C.L., Brooks S.Y., Buehler E., Chan A., Chao Q., Chen H., Cheuk R.F., Chin C.W., Chung M.K. , Conn L., Conway A.B., Conway A.R., Creasy T.H., Dewar K., Dunn P., Etgu P., Feldblyum T.V., Feng J.-D., Fong B., Fujii C.Y., Gill J.E., Goldsmith A.D., Haas B., Hansen N.F., Hughes B., Huizar L., Hunter J.L., Jenkins J., Johnson-Hopson C., Khan S., Khaykin E., Kim C.J., Koo H.L., Kremenetskaia I., Kurtz D.B., Kwan A., Lam B., Langin-Hooper S., Lee A., Lee J.M., Lenz C.A., Li J.H., Li Y.-P., Lin X., Liu S.X., Liu Z.A., Luros J.S., Maiti R., Marziali A., Militscher J., Miranda M., Nguyen M., Nierman W.C., Osborne B.I., Pai G., Peterson J., Pham P.K., Rizzo M., Rooney T., Rowley D., Sakano H., Salzberg S.L., Schwartz J.R., Shinn P., Southwick A.M., Sun H., Tallon L.J., Tambunga G., Toriumi M.J., Town C.D., Utterback T., Van Aken S., Vaysberg M., Vysotskaia V.S., Walker M., Wu D., Yu G., Fraser C.M., Venter J.C., Davis R.W. Nature 408:816-820(2000) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: cv. Columbia.
[3]	The Arabidopsis Information Resource (TAIR) Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases Cited for: GENOME REANNOTATION. Strain: cv. Columbia.
[4]	"Functional annotation of a full-length Arabidopsis cDNA collection." Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T., Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y., Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K., Shinagawa A., Shinozaki K. Science 296:141-145(2002) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[5]	"Empirical analysis of transcriptional activity in the Arabidopsis genome." Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G. , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R. Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA]. Strain: cv. Columbia.
[6]	"Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs." Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A., Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y., Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K. , Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y., Shinozaki K. Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 427-790. Strain: cv. Columbia.
[7]	"An evolutionarily conserved translation initiation mechanism regulates nuclear or mitochondrial targeting of DNA ligase 1 in Arabidopsis thaliana." Sunderland P.A., West C.E., Waterworth W.M., Bray C.M. Plant J. 47:356-367(2006) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION OF ISOFORMS 1; 2 AND 3, SUBCELLULAR LOCATION. Strain: cv. Columbia.
[8]	"Genome-wide analysis of the core DNA replication machinery in the higher plants Arabidopsis and rice." Shultz R.W., Tatineni V.M., Hanley-Bowdoin L., Thompson W.F. Plant Physiol. 144:1697-1714(2007) [PubMed] [Europe PMC] [Abstract] Cited for: REVIEW.
[9]	"DNA ligase 1 deficient plants display severe growth defects and delayed repair of both DNA single and double strand breaks." Waterworth W.M., Kozak J., Provost C.M., Bray C.M., Angelis K.J., West C.E. BMC Plant Biol. 9:79-79(2009) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, DISRUPTION PHENOTYPE. Strain: cv. Columbia.
[10]	"DNA LIGASE I exerts a maternal effect on seed development in Arabidopsis thaliana." Andreuzza S., Li J., Guitton A.-E., Faure J.-E., Casanova S., Park J.-S., Choi Y., Chen Z., Berger F. Development 137:73-81(2010) [PubMed] [Europe PMC] [Abstract] Cited for: FUNCTION, TISSUE SPECIFICITY, SUBCELLULAR LOCATION, DEVELOPMENTAL STAGE.
+	Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	X97924 mRNA. Translation: CAA66599.1. AC011438 Genomic DNA. Translation: AAF18258.1. Sequence problems. AC026875 Genomic DNA. Translation: AAF79833.1. Sequence problems. CP002684 Genomic DNA. Translation: AEE28251.1. AK117238 mRNA. Translation: BAC41914.1. BT005964 mRNA. Translation: AAO64899.1. AK222166 mRNA. Translation: BAD95276.1. Different initiation.
IPI	IPI00535474.
PIR	S71278.
RefSeq	NP_172293.2. NM_100689.4.
UniGene	At.36.
3D structure databases
ProteinModelPortal	Q42572.
SMR	Q42572. Positions 159-776.
ModBase	Search...
Protein-protein interaction databases
STRING	3702.AT1G08130.1-P.
Proteomic databases
PaxDb	Q42572.
PRIDE	Q42572.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblPlants	AT1G08130.1; AT1G08130.1; AT1G08130.
GeneID	837333.
KEGG	ath:AT1G08130.
Organism-specific databases
TAIR	At1g08130.
Phylogenomic databases
eggNOG	COG1793.
HOGENOM	HOG000036006.
InParanoid	Q42572.
KO	K10747.
OMA	AQVACLY.
PhylomeDB	Q42572.
ProtClustDB	PLN03113.
Gene expression databases
ArrayExpress	Q42572.
Genevestigator	Q42572.
GermOnline	AT1G08130. Arabidopsis thaliana.
Family and domain databases
Gene3D	1.10.3260.10. 1 hit. 2.40.50.140. 1 hit.
InterPro	IPR000977. DNA_ligase_ATP-dep. IPR012309. DNA_ligase_ATP-dep_C. IPR012310. DNA_ligase_ATP-dep_cent. IPR016059. DNA_ligase_ATP-dep_CS. IPR012308. DNA_ligase_ATP-dep_N. IPR012340. NA-bd_OB-fold. [Graphical view]
Pfam	PF04679. DNA_ligase_A_C. 1 hit. PF01068. DNA_ligase_A_M. 1 hit. PF04675. DNA_ligase_A_N. 1 hit. [Graphical view]
SUPFAM	SSF50249. Nucleic_acid_OB. 1 hit. SSF117018. SSF117018. 1 hit.
TIGRFAMs	TIGR00574. dnl1. 1 hit.
PROSITE	PS00697. DNA_LIGASE_A1. 1 hit. PS00333. DNA_LIGASE_A2. 1 hit. PS50160. DNA_LIGASE_A3. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DNLI1_ARATH

Accession

Primary (citable) accession number: Q42572
Secondary accession number(s): Q541Y6 , Q56W81, Q9LMZ4, Q9SGE5

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	January 10, 2003
Last modified:	May 1, 2013
This is version 102 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Plant Protein Annotation Program