DNA ligase 3 - Dictyostelium discoideum (Slime mold)

Preferred order of sections

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) [Reference proteome]

Taxonomic identifier

44689 [NCBI]

Taxonomic lineage

Eukaryota › Amoebozoa › Mycetozoa › Dictyosteliida › Dictyostelium

Protein attributes

Sequence length	1175 AA.
Sequence status	Complete.
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 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 cell cycle Inferred from electronic annotation. Source: UniProtKB-KW cell division Inferred from electronic annotation. Source: UniProtKB-KW lagging strand elongation Inferred from Biological aspect of Ancestor. Source: RefGenome nucleotide-excision repair Inferred from Biological aspect of Ancestor. Source: RefGenome
Cellular_component	chromosome Inferred from Biological aspect of Ancestor. Source: RefGenome nucleus Inferred from Biological aspect of Ancestor. Source: RefGenome
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...

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)

Tools

Q54QM4 [UniParc].

Last modified May 24, 2005. Version 1.
Checksum: D963D7D6EF49547E
Show »

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

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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.

Kuspa A.
Nature 435:43-57(2005) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: AX4.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AAFI02000057 Genomic DNA. Translation: EAL65543.1.
RefSeq	XP_638847.1. XM_633755.1.
3D structure databases
ProteinModelPortal	Q54QM4.
ModBase	Search...
Protein-protein interaction databases
STRING	44689.DDB_0232266.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
EnsemblProtists	DDB0232266; DDB0232266; DDB_G0283857.
GeneID	8624245.
KEGG	ddi:DDB_G0283857.
Organism-specific databases
dictyBase	DDB_G0283857. lig3.
Phylogenomic databases
eggNOG	COG1793.
KO	K10776.
OMA	INTGAKF.
ProtClustDB	CLSZ2736577.
Family and domain databases
Gene3D	2.40.50.140. 1 hit. 3.40.50.10190. 2 hits.
InterPro	IPR001357. BRCT_dom. 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	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]
SUPFAM	SSF52113. BRCT. 2 hits. SSF50249. Nucleic_acid_OB. 1 hit.
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:	May 29, 2013
This is version 58 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Relevant documents

Dictyostelium discoideum

Dictyostelium discoideum: entries, gene names and cross-references to dictyBase

SIMILARITY comments

Index of protein domains and families

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Family and domain databases

Entry information

Relevant documents