Reviewed, UniProtKB/Swiss-Prot Q9LL84 (DNLI4_ARATH)

Names and origin

Protein names

Recommended name:
    DNA ligase 4
    EC=6.5.1.1
Alternative name(s):
    DNA ligase IV
    Polydeoxyribonucleotide synthase [ATP] 4

Gene names

Name:	LIG4
Ordered Locus Names:	At5g57160
ORF Names:	MUL3.11

Organism

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

Taxonomic identifier

3702 [NCBI]

Taxonomic lineage

Eukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › eudicotyledons › core eudicotyledons › rosids › eurosids II › Brassicales › Brassicaceae › Arabidopsis

Protein attributes

Sequence length	1219 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Efficiently joins single-strand breaks in a double-stranded polydeoxynucleotide in an ATP-dependent reaction. Involved in DNA nonhomologous end joining (NHEJ) required for double-strand break repair. May be involved for T-DNA integration even if not absolutely required. Seems to be dispensable under normal growth conditions. Ref.3 Ref.5
Catalytic activity	ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).
Cofactor	Magnesium By similarity.
Subunit structure	Interacts with XRCC4 via its tandem BRCT domains. Ref.1
Subcellular location	Nucleus By similarity.
Tissue specificity	Widely expressed, with higher levels in young flowers and roots. Ref.1
Induction	Induced by gamma radiation and by white light, but not by UV-B. Regulated by ATM in response to DNA double strand breaks (DSBs). Ref.1 Ref.4
Sequence similarities	Belongs to the ATP-dependent DNA ligase family. Contains 2 BRCT domains.
Sequence caution	The sequence BAA97366.1 differs from that shown. Reason: Erroneous gene model prediction.

Ontologies

Keywords
Biological process	DNA damage DNA recombination DNA repair DNA replication
Cellular component	Nucleus
Domain	Repeat
Ligand	ATP-binding Magnesium Metal-binding Nucleotide-binding
Molecular function	Ligase
Technical term	Complete proteome
Gene Ontology (GO)
Biological process	DNA recombination Inferred from electronic annotation. Source: UniProtKB-KW DNA replication Inferred from electronic annotation. Source: UniProtKB-KW double-strand break repair Inferred from mutant phenotype. Source: TAIR response to X-ray Ref.3 Inferred from mutant phenotype. Source: TAIR
Cellular component	nucleus Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA binding Inferred from electronic annotation. Source: InterPro DNA ligase (ATP) activity Ref.1 Inferred from direct assay. Source: TAIR magnesium ion binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Ref.1 Inferred from physical interaction. Source: TAIR
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1219	1219	DNA ligase 4		PRO_0000059580
Regions
	Domain	651 – 739	89	BRCT 1
	Domain	807 – 909	103	BRCT 2
Sites
	Active site	253	1	N6-AMP-lysine intermediate By similarity
	Metal binding	303	1	Magnesium 1 Potential
	Metal binding	418	1	Magnesium 2 Potential
	Binding site	251	1	ATP By similarity
	Binding site	258	1	ATP By similarity
	Binding site	273	1	ATP By similarity
	Binding site	423	1	ATP By similarity
	Binding site	434	1	ATP By similarity
	Binding site	440	1	ATP By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q9LL84-1 [UniParc]. Last modified October 1, 2000. Version 1. Checksum: 97825B4B795E45FB	FASTA	1,219	137,851
	10 20 30 40 50 60 MTEEIKFSVL VSLFNWIQKS KTSSQKRSKF RKFLDTYCKP SDYFVAVRLI IPSLDRERGS 70 80 90 100 110 120 YGLKESVLAT CLIDALGISR DAPDAVRLLN WRKGGTAKAG ANAGNFSLIA AEVLQRRQGM 130 140 150 160 170 180 ASGGLTIKEL NDLLDRLASS ENRAEKTLVL STLIQKTNAQ EMKWVIRIIL KDLKLGMSEK 190 200 210 220 230 240 SIFQEFHPDA EDLFNVTCDL KLVCEKLRDR HQRHKRQDIE VGKAVRPQLA MRIGDVNAAW 250 260 270 280 290 300 KKLHGKDVVA ECKFDGDRIQ IHKNGTDIHY FSRNFLDHSE YAHAMSDLIV QNILVDKCIL 310 320 330 340 350 360 DGEMLVWDTS LNRFAEFGSN QEIAKAAREG LDSHKQLCYV AFDVLYVGDT SVIHQSLKER 370 380 390 400 410 420 HELLKKVVKP LKGRLEVLVP EGGLNVHRPS GEPSWSIVVH AAADVERFFK ETVENRDEGI 430 440 450 460 470 480 VLKDLESKWE PGDRSGKWMK LKPEYIRAGA DLDVLIIGGY YGSGRRGGEV AQFLVALADR 490 500 510 520 530 540 AEANVYPRRF MSFCRVGTGL SDDELNTVVS KLKPYFRKNE HPKKAPPSFY QVTNHSKERP 550 560 570 580 590 600 DVWIDSPEKS IILSITSDIR TIRSEVFVAP YSLRFPRIDK VRYDKPWHEC LDVQAFVELV 610 620 630 640 650 660 NSSNGTTQKQ KESESTQDNP KVNKSSKRGE KKNVSLVPSQ FIQTDVSDIK GKTSIFSNMI 670 680 690 700 710 720 FYFVNVPRSH SLETFHKMVV ENGGKFSMNL NNSVTHCIAA ESSGIKYQAA KRQRDVIHFS 730 740 750 760 770 780 WVLDCCSRNK MLPLLPKYFL HLTDASRTKL QDDIDEFSDS YYWDLDLEGL KQVLSNAKQS 790 800 810 820 830 840 EDSKSIDYYK KKLCPEKRWS CLLSCCVYFY PYSQTLSTEE EALLGIMAKR LMLEVLMAGG 850 860 870 880 890 900 KVSNNLAHAS HLVVLAMAEE PLDFTLVSKS FSEMEKRLLL KKRLHVVSSH WLEESLQREE 910 920 930 940 950 960 KLCEDVYTLR PKYMEESDTE ESDKSEHDTT EVASQGSAQT KEPASSKIAI TSSRGRSNTR 970 980 990 1000 1010 1020 AVKRGRSSTN SLQRVQRRRG KQPSKISGDE TEESDASEEK VSTRLSDIAE ETDSFGEAQR 1030 1040 1050 1060 1070 1080 NSSRGKCAKR GKSRVGQTQR VQRSRRGKKA AKIGGDESDE NDELDGNNNV SADAEEGNAA 1090 1100 1110 1120 1130 1140 GRSVENEETR EPDIAKYTES QQRDNTVAVE EALQDSRNAK TEMDMKEKLQ IHEDPLQAML 1150 1160 1170 1180 1190 1200 MKMFPIPSQK TTETSNRTTG EYRKANVSGE CESSEKRKLD AETDNTSVNA GAESDVVPPL 1210 VKKKKVSYRD VAGELLKDW

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"Arabidopsis DNA ligase IV is induced by gamma-irradiation and interacts with an Arabidopsis homologue of the double strand break repair protein XRCC4." West C.E., Waterworth W.M., Jiang Q., Bray C.M. Plant J. 24:67-78(2000) [PubMed: 11029705] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA], INDUCTION, TISSUE SPECIFICITY, INTERACTION WITH XRCC4.
[2]	"Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence features of the regions of 3,076,755 bp covered by sixty P1 and TAC clones." Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Kotani H., Tabata S. DNA Res. 7:31-63(2000) [PubMed: 10718197] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
[3]	"The Arabidopsis AtLIG4 gene is required for the repair of DNA damage, but not for the integration of Agrobacterium T-DNA." van Attikum H., Bundock P., Overmeer R.M., Lee L.-Y., Gelvin S.B., Hooykaas P.J.J. Nucleic Acids Res. 31:4247-4255(2003) [PubMed: 12853643] [Abstract] Cited for: FUNCTION.
[4]	"AtATM is essential for meiosis and the somatic response to DNA damage in plants." Garcia V., Bruchet H., Camescasse D., Granier F., Bouchez D., Tissier A. Plant Cell 15:119-132(2003) [PubMed: 12509526] [Abstract] Cited for: INDUCTION.
[5]	"Ku80- and DNA ligase IV-deficient plants are sensitive to ionizing radiation and defective in T-DNA integration." Friesner J., Britt A.B. Plant J. 34:427-440(2003) [PubMed: 12753583] [Abstract] Cited for: FUNCTION.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AF233527 mRNA. Translation: AAF91284.1. AB023042 Genomic DNA. Translation: BAA97366.1. Sequence problems.
IPI	IPI00524567.
RefSeq	NP_568851.2.
UniGene	At.69713
3D structure databases
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9LL84. 1 interaction.
Proteomic databases
PRIDE	Q9LL84.
Genome annotation databases
GeneID	835822.
GenomeReviews	Gene locus AT5G57160 in contig BA000015_GR.
KEGG	ath:AT5G57160.
NMPDR	fig|3702.1.peg.27664.
Organism-specific databases
GeneFarm	4927.
TAIR	At5g57160.
Phylogenomic databases
OMA	Q9LL84. TSDIRTI.
Enzyme and pathway databases
BRENDA	6.5.1.1. 302.
Gene expression databases
GermOnline	AT5G57160. Arabidopsis thaliana.
Family and domain databases
InterPro	IPR001357. BRCT. IPR000977. DNA_ligase. IPR012309. DNA_ligase_A_C. IPR012310. DNA_ligase_A_M. IPR012308. DNA_ligase_A_N. IPR016059. DNA_ligase_CS. IPR012340. NA-bd_OB-fold. [Graphical view]
Gene3D	G3DSA:2.40.50.140. OB_NA_bd_sub. 1 hit.
Pfam	PF00533. BRCT. 2 hits. PF04679. DNA_ligase_A_C. 1 hit. PF01068. DNA_ligase_A_M. 1 hit. PF04675. DNA_ligase_A_N. 1 hit. [Graphical view]
SMART	SM00292. BRCT. 1 hit. [Graphical view]
TIGRFAMs	TIGR00574. dnl1. 1 hit.
PROSITE	PS50172. BRCT. 2 hits. 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

DNLI4_ARATH

Accession

Primary (citable) accession number: Q9LL84
Secondary accession number(s): Q9LU70

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 24, 2006
Last sequence update:	October 1, 2000
Last modified:	June 16, 2009
This is version 53 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

PPAP (Plant Proteome Annotation Project)