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Q54CR9

- DNLI4_DICDI

UniProt

Q54CR9 - DNLI4_DICDI

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Protein
DNA ligase 4
Gene
lig4, DDB_G0292760
Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed - Annotation score: 4 out of 5 - Protein inferred from homologyi

Functioni

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 activityi

ATP + (deoxyribonucleotide)(n) + (deoxyribonucleotide)(m) = AMP + diphosphate + (deoxyribonucleotide)(n+m).

Cofactori

Magnesium By similarity.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei414 – 4141ATP By similarity
Active sitei416 – 4161N6-AMP-lysine intermediate By similarity
Binding sitei421 – 4211ATP By similarity
Binding sitei436 – 4361ATP By similarity
Metal bindingi467 – 4671Magnesium 1 Reviewed prediction
Metal bindingi574 – 5741Magnesium 2 Reviewed prediction
Binding sitei579 – 5791ATP By similarity
Binding sitei590 – 5901ATP By similarity
Binding sitei596 – 5961ATP By similarity

GO - Molecular functioni

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

GO - Biological processi

  1. DNA ligation Source: RefGenome
  2. DNA recombination Source: UniProtKB-KW
  3. double-strand break repair via nonhomologous end joining Source: RefGenome
  4. lagging strand elongation Source: RefGenome
  5. nucleotide-excision repair Source: RefGenome
  6. single strand break repair Source: dictyBase
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

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 4 (EC:6.5.1.1)
Alternative name(s):
DNA ligase IV
Polydeoxyribonucleotide synthase [ATP] 4
Gene namesi
Name:lig4
ORF Names:DDB_G0292760
OrganismiDictyostelium discoideum (Slime mold)
Taxonomic identifieri44689 [NCBI]
Taxonomic lineageiEukaryotaAmoebozoaMycetozoaDictyosteliidaDictyostelium
ProteomesiUP000002195: Chromosome 6, UP000002195: Unassembled WGS sequence

Organism-specific databases

dictyBaseiDDB_G0292760. lig4.

Subcellular locationi

Nucleus By similarity

GO - Cellular componenti

  1. DNA ligase IV complex Source: RefGenome
  2. DNA-dependent protein kinase-DNA ligase 4 complex Source: dictyBase
  3. chromosome Source: RefGenome
  4. nucleus Source: dictyBase
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 10881088DNA ligase 4
PRO_0000351216Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi44689.DDB_0232255.

Structurei

3D structure databases

ProteinModelPortaliQ54CR9.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini827 – 91791BRCT 1
Add
BLAST
Domaini984 – 1088105BRCT 2
Add
BLAST

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi39 – 5214Poly-Asn
Add
BLAST
Compositional biasi72 – 787Poly-Thr
Compositional biasi110 – 12314Poly-Thr
Add
BLAST
Compositional biasi969 – 9757Poly-Thr

Sequence similaritiesi

Contains 2 BRCT domains.

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiCOG1793.
KOiK10777.
OMAiHMCPSTK.
PhylomeDBiQ54CR9.

Family and domain databases

Gene3Di1.10.3260.10. 1 hit.
2.40.50.140. 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.
IPR012308. DNA_ligase_ATP-dep_N.
IPR021536. DNA_ligase_IV_dom.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PfamiPF00533. 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]
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.
PS50160. DNA_LIGASE_A3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q54CR9-1 [UniParc]FASTAAdd to Basket

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MALSLYYDED DDENENENKD KPNNDFKNQQ QINTSKTTNN NNNINNKNNY     50
NNKFNDDDIF NNDKIITKPR VTTTTTTTKN TSTNSNINKT KFNDDDIFDD 100
EDEDSNSNKT TTTTTTTTTT TDTIITNDYR YQKTVPFSSF CDLMNRIIND 150
TKISNKKNYL EKFMNHYKDE PNNFYQLLRL ILPQLDKDRN SYGLKEKTLA 200
RLYVELLNIS PESVDAMRLL NWKKSTNDEI GGDFGTAVYL SLKNRCNNDN 250
GRIKVSMGDI NESLDQLSQP LTDKKTKVSI LKKVLRSTTA QEQKWFVRII 300
LKEMKNGLSD NITLKFFHPD AIDHFNITSN LRLVCTNLFY MTQSKQKELK 350
DKQKLEEKEN LLKQQQQQQN DLDIYKLEIK LFNPIKPMLA NRQSIDNLSM 400
ILNSAISATQ FVVEKKFDGE RIQIHKDGEQ VKYFSRNSND STGIYGSMFT 450
PIVKECVLAE RCILDGELIV WDSISQRFED FGNLKTLALN KDGISGSGDP 500
LGINYGKQLC FIAFDILFVK DQSVMNLPLM QRLMLLKRCV TIKSKQFEIS 550
EQTTVNSISQ IISLLESAII NREEGLMLKN LHSLYVPAER KDKWVKIKPE 600
YIDGMGNGAD DLDLVIIGGY YGSGLNRRGG TISHFMLGVP FIADSTDTDI 650
DDESTFDKNV IFYSFCKVGS GYTDIQLKSL QKDLDPHWNN FSTSKPPSII 700
QLAEPFKEKP DVWIDPRVYS KVLQIKASQI VVTDKYKCGY TLRFPRVLKI 750
RDDKGWKDCC SHEEIIDLFT NYSTNLNFKR DHEYGDGSGG KNKKLKKSKK 800
TTNQLLADSG LKVLSIFQDT DTSGIIPTQN IFQGIEICVI KGSSGEYTKS 850
KLEIMIVEMG GSKVQYPSRN TNYVISSKEV VKIQNLIQSG FIDIVSFNWI 900
VDCYNEKRLV PLGPKYMIFS TESTKKRFLL DSDQFGDSYI NETTEQSLKD 950
SFNQIDKLKL KKQLSINSTT TTTTTSISKY FSNCWWSLFK EFTFYLDLYQ 1000
VVGEKSTLIE NNNLELSNLN IQFYGGKISI EFNNKITHVV LDSLDLSRIT 1050
FIKNKINSLS LPIQIVTTNW IQLSINNYSI QPILEILD 1088
Length:1,088
Mass (Da):124,791
Last modified:May 24, 2005 - v1
Checksum:iFE1B3C00A20B5E76
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AAFI02000196 Genomic DNA. Translation: EAL61054.1.
RefSeqiXP_629472.1. XM_629470.1.

Genome annotation databases

EnsemblProtistsiDDB0232255; DDB0232255; DDB_G0292760.
GeneIDi8628862.
KEGGiddi:DDB_G0292760.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
AAFI02000196 Genomic DNA. Translation: EAL61054.1 .
RefSeqi XP_629472.1. XM_629470.1.

3D structure databases

ProteinModelPortali Q54CR9.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 44689.DDB_0232255.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblProtistsi DDB0232255 ; DDB0232255 ; DDB_G0292760 .
GeneIDi 8628862.
KEGGi ddi:DDB_G0292760.

Organism-specific databases

dictyBasei DDB_G0292760. lig4.

Phylogenomic databases

eggNOGi COG1793.
KOi K10777.
OMAi HMCPSTK.
PhylomeDBi Q54CR9.

Miscellaneous databases

PROi Q54CR9.

Family and domain databases

Gene3Di 1.10.3260.10. 1 hit.
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.
IPR012308. DNA_ligase_ATP-dep_N.
IPR021536. DNA_ligase_IV_dom.
IPR012340. NA-bd_OB-fold.
[Graphical view ]
Pfami 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 ]
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.
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 nameiDNLI4_DICDI
AccessioniPrimary (citable) accession number: Q54CR9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: September 23, 2008
Last sequence update: May 24, 2005
Last modified: September 3, 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

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