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Q54CR9

- DNLI4_DICDI

UniProt

Q54CR9 - DNLI4_DICDI

Protein

DNA ligase 4

Gene

lig4

Organism
Dictyostelium discoideum (Slime mold)
Status
Reviewed - Annotation score: 4 out of 5- Protein inferred from homologyi
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    • History
      Entry version 67 (01 Oct 2014)
      Sequence version 1 (24 May 2005)
      Previous versions | rss
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    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.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 – 4141ATPBy similarity
    Active sitei416 – 4161N6-AMP-lysine intermediateBy similarity
    Binding sitei421 – 4211ATPBy similarity
    Binding sitei436 – 4361ATPBy similarity
    Metal bindingi467 – 4671Magnesium 1Sequence Analysis
    Metal bindingi574 – 5741Magnesium 2Sequence Analysis
    Binding sitei579 – 5791ATPBy similarity
    Binding sitei590 – 5901ATPBy similarity
    Binding sitei596 – 5961ATPBy 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

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

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

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

    Interactioni

    Protein-protein interaction databases

    STRINGi44689.DDB_0232255.

    Structurei

    3D structure databases

    ProteinModelPortaliQ54CR9.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini827 – 91791BRCT 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini984 – 1088105BRCT 2PROSITE-ProRule annotationAdd
    BLAST

    Compositional bias

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

    Sequence similaritiesi

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

    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

    « Hide

    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: October 1, 2014
    This is version 67 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