Q54CR9 (DNLI4_DICDI) Reviewed, UniProtKB/Swiss-Prot

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
ORF Names:	DDB_G0292760

Organism

Dictyostelium discoideum (Slime mold) [Reference proteome]

Taxonomic identifier

44689 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Amoebozoa › Mycetozoa › Dictyosteliida › Dictyostelium

Protein attributes

Sequence length	1088 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

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 By similarity.
Catalytic activity	ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).
Cofactor	Magnesium By similarity.
Subcellular location	Nucleus By similarity.
Sequence similarities	Belongs to the ATP-dependent DNA ligase family. Contains 2 BRCT domains.

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 Reference proteome
Gene Ontology (GO)
Biological_process	DNA recombination Inferred from electronic annotation. Source: UniProtKB-KW double-strand break repair via nonhomologous end joining Inferred from Biological aspect of Ancestor. Source: RefGenome lagging strand elongation Inferred from Biological aspect of Ancestor. Source: RefGenome nucleotide-excision repair Inferred from Biological aspect of Ancestor. Source: RefGenome single strand break repair Inferred from sequence or structural similarity PubMed 16112620. Source: dictyBase
Cellular_component	DNA ligase IV complex Inferred from Biological aspect of Ancestor. Source: RefGenome DNA-dependent protein kinase-DNA ligase 4 complex Inferred from sequence or structural similarity PubMed 16112620PubMed 16582628. Source: dictyBase chromosome Inferred from Biological aspect of Ancestor. Source: RefGenome
Molecular_function	ATP binding Inferred from electronic annotation. Source: UniProtKB-KW DNA binding Inferred from sequence or structural similarity PubMed 16112620. Source: dictyBase DNA ligase (ATP) activity Inferred from sequence or structural similarity PubMed 16112620. Source: dictyBase metal ion binding Inferred from electronic annotation. Source: UniProtKB-KW
Complete GO annotation...

Sequence annotation (Features)

	Feature key	Position(s)	Length	Description	Graphical view	Feature identifier
Molecule processing
	Chain	1 – 1088	1088	DNA ligase 4		PRO_0000351216
Regions
	Domain	827 – 917	91	BRCT 1
	Domain	984 – 1088	105	BRCT 2
	Compositional bias	39 – 52	14	Poly-Asn
	Compositional bias	72 – 78	7	Poly-Thr
	Compositional bias	110 – 123	14	Poly-Thr
	Compositional bias	969 – 975	7	Poly-Thr
Sites
	Active site	416	1	N6-AMP-lysine intermediate By similarity
	Metal binding	467	1	Magnesium 1 Potential
	Metal binding	574	1	Magnesium 2 Potential
	Binding site	414	1	ATP By similarity
	Binding site	421	1	ATP By similarity
	Binding site	436	1	ATP By similarity
	Binding site	579	1	ATP By similarity
	Binding site	590	1	ATP By similarity
	Binding site	596	1	ATP By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q54CR9 [UniParc]. Last modified May 24, 2005. Version 1. Checksum: FE1B3C00A20B5E76	FASTA	1,088	124,791
	10 20 30 40 50 60 MALSLYYDED DDENENENKD KPNNDFKNQQ QINTSKTTNN NNNINNKNNY NNKFNDDDIF 70 80 90 100 110 120 NNDKIITKPR VTTTTTTTKN TSTNSNINKT KFNDDDIFDD EDEDSNSNKT TTTTTTTTTT 130 140 150 160 170 180 TDTIITNDYR YQKTVPFSSF CDLMNRIIND TKISNKKNYL EKFMNHYKDE PNNFYQLLRL 190 200 210 220 230 240 ILPQLDKDRN SYGLKEKTLA RLYVELLNIS PESVDAMRLL NWKKSTNDEI GGDFGTAVYL 250 260 270 280 290 300 SLKNRCNNDN GRIKVSMGDI NESLDQLSQP LTDKKTKVSI LKKVLRSTTA QEQKWFVRII 310 320 330 340 350 360 LKEMKNGLSD NITLKFFHPD AIDHFNITSN LRLVCTNLFY MTQSKQKELK DKQKLEEKEN 370 380 390 400 410 420 LLKQQQQQQN DLDIYKLEIK LFNPIKPMLA NRQSIDNLSM ILNSAISATQ FVVEKKFDGE 430 440 450 460 470 480 RIQIHKDGEQ VKYFSRNSND STGIYGSMFT PIVKECVLAE RCILDGELIV WDSISQRFED 490 500 510 520 530 540 FGNLKTLALN KDGISGSGDP LGINYGKQLC FIAFDILFVK DQSVMNLPLM QRLMLLKRCV 550 560 570 580 590 600 TIKSKQFEIS EQTTVNSISQ IISLLESAII NREEGLMLKN LHSLYVPAER KDKWVKIKPE 610 620 630 640 650 660 YIDGMGNGAD DLDLVIIGGY YGSGLNRRGG TISHFMLGVP FIADSTDTDI DDESTFDKNV 670 680 690 700 710 720 IFYSFCKVGS GYTDIQLKSL QKDLDPHWNN FSTSKPPSII QLAEPFKEKP DVWIDPRVYS 730 740 750 760 770 780 KVLQIKASQI VVTDKYKCGY TLRFPRVLKI RDDKGWKDCC SHEEIIDLFT NYSTNLNFKR 790 800 810 820 830 840 DHEYGDGSGG KNKKLKKSKK TTNQLLADSG LKVLSIFQDT DTSGIIPTQN IFQGIEICVI 850 860 870 880 890 900 KGSSGEYTKS KLEIMIVEMG GSKVQYPSRN TNYVISSKEV VKIQNLIQSG FIDIVSFNWI 910 920 930 940 950 960 VDCYNEKRLV PLGPKYMIFS TESTKKRFLL DSDQFGDSYI NETTEQSLKD SFNQIDKLKL 970 980 990 1000 1010 1020 KKQLSINSTT TTTTTSISKY FSNCWWSLFK EFTFYLDLYQ VVGEKSTLIE NNNLELSNLN 1030 1040 1050 1060 1070 1080 IQFYGGKISI EFNNKITHVV LDSLDLSRIT FIKNKINSLS LPIQIVTTNW IQLSINNYSI QPILEILD

References

[1]

"The genome of the social amoeba Dictyostelium discoideum." Eichinger L., Pachebat J.A., Gloeckner G., Rajandream M.A., Sucgang R., Berriman M., Song J., Olsen R., Szafranski K., Xu Q., Tunggal B., Kummerfeld S., Madera M., Konfortov B.A., Rivero F., Bankier A.T., Lehmann R., Hamlin N. , Davies R., Gaudet P., Fey P., Pilcher K., Chen G., Saunders D., Sodergren E.J., Davis P., Kerhornou A., Nie X., Hall N., Anjard C., Hemphill L., Bason N., Farbrother P., Desany B., Just E., Morio T., Rost R., Churcher C.M., Cooper J., Haydock S., van Driessche N., Cronin A., Goodhead I., Muzny D.M., Mourier T., Pain A., Lu M., Harper D., Lindsay R., Hauser H., James K.D., Quiles M., Madan Babu M., Saito T., Buchrieser C., Wardroper A., Felder M., Thangavelu M., Johnson D., Knights A., Loulseged H., Mungall K.L., Oliver K., Price C., Quail M.A., Urushihara H., Hernandez J., Rabbinowitsch E., Steffen D., Sanders M., Ma J., Kohara Y., Sharp S., Simmonds M.N., Spiegler S., Tivey A., Sugano S., White B., Walker D., Woodward J.R., Winckler T., Tanaka Y., Shaulsky G., Schleicher M., Weinstock G.M., Rosenthal A., Cox E.C., Chisholm R.L., Gibbs R.A., Loomis W.F., Platzer M., Kay R.R., Williams J.G., Dear P.H., Noegel A.A., Barrell B.G., Kuspa A. Nature 435:43-57(2005) [PubMed] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: AX4.

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Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AAFI02000196 Genomic DNA. Translation: EAL61054.1.
RefSeq	XP_629472.1. XM_629470.1.
3D structure databases
HSSP	HSSP built from PDB template 1Z56 based on UniProtKB Q08387.
ProteinModelPortal	Q54CR9.
ModBase	Search...
Protein-protein interaction databases
STRING	44689.DDB_0232255.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblProtists	DDB0232255; DDB0232255; DDB_G0292760.
GeneID	8628862.
KEGG	ddi:DDB_G0292760.
Organism-specific databases
dictyBase	DDB_G0292760. lig4.
Phylogenomic databases
eggNOG	COG1793.
KO	K10777.
OMA	HMCPSTK.
ProtClustDB	CLSZ2728715.
Family and domain databases
Gene3D	1.10.3260.10. 1 hit. 2.40.50.140. 1 hit.
InterPro	IPR001357. BRCT_dom. IPR000977. DNA_ligase_ATP-dep. IPR012309. DNA_ligase_ATP-dep_C. IPR012310. DNA_ligase_ATP-dep_cent. IPR012308. DNA_ligase_ATP-dep_N. IPR021536. DNA_ligase_IV. IPR012340. NA-bd_OB-fold. [Graphical view]
Pfam	PF00533. BRCT. 1 hit. PF04679. DNA_ligase_A_C. 1 hit. PF01068. DNA_ligase_A_M. 1 hit. PF04675. DNA_ligase_A_N. 1 hit. PF11411. DNA_ligase_IV. 1 hit. [Graphical view]
SMART	SM00292. BRCT. 2 hits. [Graphical view]
SUPFAM	SSF52113. BRCT. 1 hit. SSF50249. Nucleic_acid_OB. 1 hit.
TIGRFAMs	TIGR00574. dnl1. 1 hit.
PROSITE	PS50172. BRCT. 2 hits. PS50160. DNA_LIGASE_A3. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

DNLI4_DICDI

Accession

Primary (citable) accession number: Q54CR9

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 23, 2008
Last sequence update:	May 24, 2005
Last modified:	May 1, 2013
This is version 60 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)