Reviewed, UniProtKB/Swiss-Prot Q54QM4 (DNLI3_DICDI)

Names and origin

Protein names

Recommended name:
    DNA ligase 3
    EC=6.5.1.1
Alternative name(s):
    DNA ligase III
    Polydeoxyribonucleotide synthase [ATP] 3

Gene names

Name:	lig3
ORF Names:	DDB_G0283857

Organism

Dictyostelium discoideum (Slime mold) [Complete proteome]

Taxonomic identifier

44689 [NCBI]

Taxonomic lineage

Eukaryota › Amoebozoa › Mycetozoa › Dictyosteliida › Dictyostelium

Protein attributes

Sequence length	1175 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Inferred from homology.

General annotation (Comments)

Function	The alpha isoform interacts with DNA-repair protein XRCC1 and can correct defective DNA strand-break repair and sister chromatid exchange following treatment with ionizing radiation and alkylating agents. The beta isoform does not interact with XRCC1 and may be specifically involved in the completion of homologous recombination events that occur during meiotic prophase.
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	Cell cycle Cell division 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 repair Inferred from electronic annotation. Source: UniProtKB-KW DNA replication Inferred from electronic annotation. Source: UniProtKB-KW cell cycle Inferred from electronic annotation. Source: UniProtKB-KW cell division Inferred from electronic annotation. Source: UniProtKB-KW
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 Inferred from electronic annotation. Source: EC magnesium 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 – 1175	1175	DNA ligase 3		PRO_0000351215
Regions
	Domain	883 – 976	94	BRCT 1
	Domain	1067 – 1174	108	BRCT 2
	Compositional bias	196 – 224	29	Asp-rich
	Compositional bias	225 – 229	5	Poly-Lys
	Compositional bias	622 – 635	14	Thr-rich
	Compositional bias	647 – 655	9	Poly-Asp
	Compositional bias	658 – 661	4	Poly-Gln
	Compositional bias	851 – 859	9	Poly-Ser
	Compositional bias	987 – 996	10	Poly-Ser
	Compositional bias	1016 – 1019	4	Poly-Gln
	Compositional bias	1051 – 1060	10	Poly-Asn
	Compositional bias	1117 – 1153	37	Asn-rich
Sites
	Active site	283	1	N6-AMP-lysine intermediate By similarity
	Metal binding	334	1	Magnesium 1 Potential
	Metal binding	432	1	Magnesium 2 Potential
	Binding site	281	1	ATP By similarity
	Binding site	288	1	ATP By similarity
	Binding site	303	1	ATP By similarity
	Binding site	437	1	ATP By similarity
	Binding site	448	1	ATP By similarity
	Binding site	452	1	ATP By similarity

Sequences

	Sequence		Length	Mass (Da)
	Q54QM4-1 [UniParc]. Last modified May 24, 2005. Version 1. Checksum: D963D7D6EF49547E	FASTA	1,175	132,048
	10 20 30 40 50 60 MSEDKSGSFY SMYKLCGQLE KESSHSGKTQ LIKSFCNVFK GDLYLLAKLM LCKEDKRVFR 70 80 90 100 110 120 IKDKAMLKIC SHIWDCDLDD MIEDLDNGDF TETCKKFYIE YGKYPEKSTL TLKEVDQVLD 130 140 150 160 170 180 SLTVSGKFED QVKIINKLLK RCTPFDFRLV CRIIDSDLKI NTGAKFFLDA FHPQAYDAFK 190 200 210 220 230 240 KANNLKGVIE KIQQHDFDND NGDGDDGDGD DNDDDDGDGD SDSDKKKKKS SGGSGSDSGS 250 260 270 280 290 300 KKKSKSFEVA IKLMTPIKPM LPKAVKTVEG VVKSSECFYA EIKYDGERIQ IHKDGNQFSC 310 320 330 340 350 360 YSRNLKPLMP WKVDEVKPYI PKSTKAQQMI LDGEILLMDT KTSQPLPFGT LSAHKKNGFK 370 380 390 400 410 420 DATVCVFLFD ILYLNGKSLI HLPLKERREI LEKNVMVVKN RIEFSEVTIV NGASEKSKLT 430 440 450 460 470 480 ALLNRVFKEK LEGLVIKDAM SEYEPGCRHW IKIKKDYIHG MADSADLIAV GGYYGSGSMG 490 500 510 520 530 540 GLVTVFLMVC YDKQNKIYKT VVKASGGLDD NMIAKLQPKV TSTMTKISKE VSKIPYWLDC 550 560 570 580 590 600 PKQYAPDFIV KDIKQAMIFE IESAEFTKSD HHTTGYSMRF PRILKIRHDK DYKTATTLEE 610 620 630 640 650 660 LVEIGKDIKI VPVGKGDNNS PTTTTTTTTT TTTTTSSKLI KKQQLSDDDD DNDKDSKQQQ 670 680 690 700 710 720 QEPSKLKFVS DDLLDPFNDK SDDESNKIFI LNYVDNSGIW NEKGLSGAIG KKWPSIPKSF 730 740 750 760 770 780 SQGDSNIIKS GEIRVEKVKD DSISTNKKVF ICNLSCIIPP KSKKESYTFS LKEFKSAIKE 790 800 810 820 830 840 AKGAINQKKA SVHLAKPQFT SPSWSELDEV LTKELYNSGI KVFVHSISKS SPTTTSPTTT 850 860 870 880 890 900 SPTTTSPKIT SPSSSSSPSN KLSPLKRGRD EKLEHEIIKD IEPSLPIFED VNAVIDSKTI 910 920 930 940 950 960 DQVDVKRLIN SIKTMGGRVS DKWQQVGIGK TTHLICNGMS DLYLHVDRLG GTIVLPNWVD 970 980 990 1000 1010 1020 QCFGSDKLLP LHEDYIYFNK KDHPDYSQSS SSSSMSIEEE KIVVTTTSDD PSEGNQQQQD 1030 1040 1050 1060 1070 1080 KKVIKESKII QSKDHSSTTT IDTKITITST NNNNNGNDNN KTRKKQHLLS IFQECIIFLH 1090 1100 1110 1120 1130 1140 DNVNDRETLK RYIIAYGGDI SDSVNDKTTH LVASLPNNFS NVKPKDLFKS IINNNSKNNN 1150 1160 1170 NNNNNNNNGI IVNSLWLWDS INMSDLLDVK NYKLF

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: 15875012] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: AX4.

Cross-references

Sequence databases
EMBLGenBankDDBJ	AAFI02000057 Genomic DNA. Translation: EAL65543.1.
RefSeq	XP_638847.1.
3D structure databases
ModBase	Search...
Genome annotation databases
GeneID	3390480.
GenomeReviews	Gene locus lig3 in contig CM000153_GR.
KEGG	ddi:DDB_0232266.
Organism-specific databases
dictyBase	DDB_G0283857. lig3.
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. 2 hits. [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

DNLI3_DICDI

Accession

Primary (citable) accession number: Q54QM4

Entry history

Integrated into UniProtKB/Swiss-Prot:	September 23, 2008
Last sequence update:	May 24, 2005
Last modified:	September 22, 2009
This is version 29 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)