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Q54QM4

- DNLI3_DICDI

UniProt

Q54QM4 - DNLI3_DICDI

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Protein

DNA ligase 3

Gene

lig3

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi

Functioni

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 activityi

ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).PROSITE-ProRule annotation

Cofactori

Mg2+By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei281 – 2811ATPBy similarity
Active sitei283 – 2831N6-AMP-lysine intermediatePROSITE-ProRule annotation
Binding sitei288 – 2881ATPBy similarity
Binding sitei303 – 3031ATPBy similarity
Metal bindingi334 – 3341Magnesium 1Sequence Analysis
Metal bindingi432 – 4321Magnesium 2Sequence Analysis
Binding sitei437 – 4371ATPBy similarity
Binding sitei448 – 4481ATPBy similarity
Binding sitei452 – 4521ATPBy similarity

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. DNA binding Source: InterPro
  3. DNA ligase (ATP) activity Source: RefGenome
  4. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. cell cycle Source: UniProtKB-KW
  2. cell division Source: UniProtKB-KW
  3. DNA biosynthetic process Source: InterPro
  4. DNA ligation Source: RefGenome
  5. DNA ligation involved in DNA repair Source: InterPro
  6. DNA recombination Source: UniProtKB-KW
  7. lagging strand elongation Source: RefGenome
  8. nucleotide-excision repair Source: RefGenome
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Cell cycle, Cell division, DNA damage, DNA recombination, DNA repair, DNA replication

Keywords - Ligandi

ATP-binding, Magnesium, Metal-binding, Nucleotide-binding

Names & Taxonomyi

Protein namesi
Recommended name:
DNA ligase 3 (EC:6.5.1.1)
Alternative name(s):
DNA ligase III
Polydeoxyribonucleotide synthase [ATP] 3
Gene namesi
Name:lig3
ORF Names:DDB_G0283857
OrganismiDictyostelium discoideum (Slime mold)
Taxonomic identifieri44689 [NCBI]
Taxonomic lineageiEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium
ProteomesiUP000002195: Chromosome 4, UP000002195: Unassembled WGS sequence

Organism-specific databases

dictyBaseiDDB_G0283857. lig3.

Subcellular locationi

Nucleus By similarity

GO - Cellular componenti

  1. chromosome Source: RefGenome
  2. nucleus Source: RefGenome
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 11751175DNA ligase 3PRO_0000351215Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi44689.DDB_0232266.

Structurei

3D structure databases

ProteinModelPortaliQ54QM4.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini883 – 97694BRCT 1PROSITE-ProRule annotationAdd
BLAST
Domaini1067 – 1174108BRCT 2PROSITE-ProRule annotationAdd
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi196 – 22429Asp-richAdd
BLAST
Compositional biasi225 – 2295Poly-Lys
Compositional biasi622 – 63514Thr-richAdd
BLAST
Compositional biasi647 – 6559Poly-Asp
Compositional biasi658 – 6614Poly-Gln
Compositional biasi851 – 8599Poly-Ser
Compositional biasi987 – 99610Poly-Ser
Compositional biasi1016 – 10194Poly-Gln
Compositional biasi1051 – 106010Poly-Asn
Compositional biasi1117 – 115337Asn-richAdd
BLAST

Sequence similaritiesi

Belongs to the ATP-dependent DNA ligase family.Curated
Contains 2 BRCT domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG1793.
InParanoidiQ54QM4.
KOiK10776.
OMAiINTGAKF.
PhylomeDBiQ54QM4.

Family and domain databases

Gene3Di2.40.50.140. 1 hit.
3.40.50.10190. 2 hits.
InterProiIPR001357. 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]
PfamiPF00533. 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]
SMARTiSM00292. BRCT. 2 hits.
[Graphical view]
SUPFAMiSSF117018. SSF117018. 1 hit.
SSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 2 hits.
TIGRFAMsiTIGR00574. dnl1. 1 hit.
PROSITEiPS50172. BRCT. 2 hits.
PS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q54QM4-1 [UniParc]FASTAAdd to Basket

« Hide

        10         20         30         40         50
MSEDKSGSFY SMYKLCGQLE KESSHSGKTQ LIKSFCNVFK GDLYLLAKLM
60 70 80 90 100
LCKEDKRVFR IKDKAMLKIC SHIWDCDLDD MIEDLDNGDF TETCKKFYIE
110 120 130 140 150
YGKYPEKSTL TLKEVDQVLD SLTVSGKFED QVKIINKLLK RCTPFDFRLV
160 170 180 190 200
CRIIDSDLKI NTGAKFFLDA FHPQAYDAFK KANNLKGVIE KIQQHDFDND
210 220 230 240 250
NGDGDDGDGD DNDDDDGDGD SDSDKKKKKS SGGSGSDSGS KKKSKSFEVA
260 270 280 290 300
IKLMTPIKPM LPKAVKTVEG VVKSSECFYA EIKYDGERIQ IHKDGNQFSC
310 320 330 340 350
YSRNLKPLMP WKVDEVKPYI PKSTKAQQMI LDGEILLMDT KTSQPLPFGT
360 370 380 390 400
LSAHKKNGFK DATVCVFLFD ILYLNGKSLI HLPLKERREI LEKNVMVVKN
410 420 430 440 450
RIEFSEVTIV NGASEKSKLT ALLNRVFKEK LEGLVIKDAM SEYEPGCRHW
460 470 480 490 500
IKIKKDYIHG MADSADLIAV GGYYGSGSMG GLVTVFLMVC YDKQNKIYKT
510 520 530 540 550
VVKASGGLDD NMIAKLQPKV TSTMTKISKE VSKIPYWLDC PKQYAPDFIV
560 570 580 590 600
KDIKQAMIFE IESAEFTKSD HHTTGYSMRF PRILKIRHDK DYKTATTLEE
610 620 630 640 650
LVEIGKDIKI VPVGKGDNNS PTTTTTTTTT TTTTTSSKLI KKQQLSDDDD
660 670 680 690 700
DNDKDSKQQQ QEPSKLKFVS DDLLDPFNDK SDDESNKIFI LNYVDNSGIW
710 720 730 740 750
NEKGLSGAIG KKWPSIPKSF SQGDSNIIKS GEIRVEKVKD DSISTNKKVF
760 770 780 790 800
ICNLSCIIPP KSKKESYTFS LKEFKSAIKE AKGAINQKKA SVHLAKPQFT
810 820 830 840 850
SPSWSELDEV LTKELYNSGI KVFVHSISKS SPTTTSPTTT SPTTTSPKIT
860 870 880 890 900
SPSSSSSPSN KLSPLKRGRD EKLEHEIIKD IEPSLPIFED VNAVIDSKTI
910 920 930 940 950
DQVDVKRLIN SIKTMGGRVS DKWQQVGIGK TTHLICNGMS DLYLHVDRLG
960 970 980 990 1000
GTIVLPNWVD QCFGSDKLLP LHEDYIYFNK KDHPDYSQSS SSSSMSIEEE
1010 1020 1030 1040 1050
KIVVTTTSDD PSEGNQQQQD KKVIKESKII QSKDHSSTTT IDTKITITST
1060 1070 1080 1090 1100
NNNNNGNDNN KTRKKQHLLS IFQECIIFLH DNVNDRETLK RYIIAYGGDI
1110 1120 1130 1140 1150
SDSVNDKTTH LVASLPNNFS NVKPKDLFKS IINNNSKNNN NNNNNNNNGI
1160 1170
IVNSLWLWDS INMSDLLDVK NYKLF
Length:1,175
Mass (Da):132,048
Last modified:May 24, 2005 - v1
Checksum:iD963D7D6EF49547E
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AAFI02000057 Genomic DNA. Translation: EAL65543.1.
RefSeqiXP_638847.1. XM_633755.1.

Genome annotation databases

EnsemblProtistsiDDB0232266; DDB0232266; DDB_G0283857.
GeneIDi8624245.
KEGGiddi:DDB_G0283857.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AAFI02000057 Genomic DNA. Translation: EAL65543.1 .
RefSeqi XP_638847.1. XM_633755.1.

3D structure databases

ProteinModelPortali Q54QM4.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 44689.DDB_0232266.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblProtistsi DDB0232266 ; DDB0232266 ; DDB_G0283857 .
GeneIDi 8624245.
KEGGi ddi:DDB_G0283857.

Organism-specific databases

dictyBasei DDB_G0283857. lig3.

Phylogenomic databases

eggNOGi COG1793.
InParanoidi Q54QM4.
KOi K10776.
OMAi INTGAKF.
PhylomeDBi Q54QM4.

Miscellaneous databases

PROi Q54QM4.

Family and domain databases

Gene3Di 2.40.50.140. 1 hit.
3.40.50.10190. 2 hits.
InterProi 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 ]
Pfami 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 ]
SMARTi SM00292. BRCT. 2 hits.
[Graphical view ]
SUPFAMi SSF117018. SSF117018. 1 hit.
SSF50249. SSF50249. 1 hit.
SSF52113. SSF52113. 2 hits.
TIGRFAMsi TIGR00574. dnl1. 1 hit.
PROSITEi PS50172. BRCT. 2 hits.
PS00697. DNA_LIGASE_A1. 1 hit.
PS00333. DNA_LIGASE_A2. 1 hit.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view ]
ProtoNeti Search...

Publicationsi

  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.

Entry informationi

Entry nameiDNLI3_DICDI
AccessioniPrimary (citable) accession number: Q54QM4
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 23, 2008
Last sequence update: May 24, 2005
Last modified: November 26, 2014
This is version 66 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Dictyostelium discoideum
    Dictyostelium discoideum: entries, gene names and cross-references to dictyBase
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3