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Q5R6L3

- DNLI4_PONAB

UniProt

Q5R6L3 - DNLI4_PONAB

Protein

DNA ligase 4

Gene

DNL4

Organism
Pongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii)
Status
Reviewed - Annotation score: 4 out of 5- Experimental evidence at transcript leveli
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    • History
      Entry version 55 (01 Oct 2014)
      Sequence version 1 (21 Dec 2004)
      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 and V(D)J recombination. The LIG4-XRCC4 complex is responsible for the NHEJ ligation step, and XRCC4 enhances the joining activity of LIG4. Binding of the LIG4-XRCC4 complex to DNA ends is dependent on the assembly of the DNA-dependent protein kinase complex DNA-PK to these DNA ends By similarity.By similarity

    Catalytic activityi

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

    Cofactori

    Magnesium.By similarity

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei271 – 2711ATPBy similarity
    Active sitei273 – 2731N6-AMP-lysine intermediatePROSITE-ProRule annotation
    Binding sitei278 – 2781ATPBy similarity
    Binding sitei293 – 2931ATPBy similarity
    Metal bindingi331 – 3311Magnesium 1Sequence Analysis
    Metal bindingi427 – 4271Magnesium 2Sequence Analysis
    Binding sitei432 – 4321ATPBy similarity
    Binding sitei443 – 4431ATPBy similarity
    Binding sitei449 – 4491ATPBy similarity

    GO - Molecular functioni

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

    GO - Biological processi

    1. cell cycle Source: UniProtKB-KW
    2. cell division Source: UniProtKB-KW
    3. DNA ligation involved in DNA repair Source: InterPro
    4. DNA recombination Source: UniProtKB-KW
    5. DNA replication Source: UniProtKB-KW

    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 4 (EC:6.5.1.1)
    Alternative name(s):
    DNA ligase IV
    Polydeoxyribonucleotide synthase [ATP] 4
    Gene namesi
    Name:DNL4
    OrganismiPongo abelii (Sumatran orangutan) (Pongo pygmaeus abelii)
    Taxonomic identifieri9601 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaePongo
    ProteomesiUP000001595: Unplaced

    Subcellular locationi

    Nucleus By similarity

    GO - Cellular componenti

    1. nonhomologous end joining complex Source: UniProtKB
    2. nucleus Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 911911DNA ligase 4PRO_0000059578Add
    BLAST

    Proteomic databases

    PRIDEiQ5R6L3.

    Interactioni

    Subunit structurei

    Binds to XRCC4. The LIG4-XRCC4 complex has probably a 1:2 stoichiometry. The LIG4-XRCC4 heteromer associates in a DNA-dependent manner with the DNA-dependent protein kinase complex DNA-PK, formed by the Ku p70/p86 dimer (G22P1/G22P2) and PRKDC. Interacts with APLF By similarity.By similarity

    Structurei

    3D structure databases

    ProteinModelPortaliQ5R6L3.
    SMRiQ5R6L3. Positions 654-759.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini654 – 74390BRCT 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini808 – 911104BRCT 2PROSITE-ProRule annotationAdd
    BLAST

    Sequence similaritiesi

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

    Keywords - Domaini

    Repeat

    Phylogenomic databases

    HOVERGENiHBG005516.
    InParanoidiQ5R6L3.
    KOiK10777.

    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.
    IPR016059. DNA_ligase_ATP-dep_CS.
    IPR012308. DNA_ligase_ATP-dep_N.
    IPR021536. DNA_ligase_IV_dom.
    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.
    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.
    PS00697. DNA_LIGASE_A1. 1 hit.
    PS00333. DNA_LIGASE_A2. 1 hit.
    PS50160. DNA_LIGASE_A3. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    Q5R6L3-1 [UniParc]FASTAAdd to Basket

    « Hide

    MAASQTSQTV ASHVPFADLC STLERIQKSK GRAEKIRHFR EFLDSWRKFH    50
    DAFHKNQKDV TDSFYPAMRL ILPQLERERM AYGIKETMLA KLYIELLNLP 100
    RDGKDALKLL NYRTPTGTHG DAGDFAMIAY FVLKPRCLQK GSLTIQQVND 150
    LLDSIASNNS AKRKDLIKKS LLQLITQSSA LEQKWLIRMI IKDLKLGVSQ 200
    QTIFSVFHSD AVELHNVTTD LEKVCRQLHD PSVGLSDISI TLFSAFKPML 250
    AAIADIEHIE KDMKHQSFYI ETKLDGERMQ MHKDGDVYKY FSRNGYNYTD 300
    QFGASPTEGS LTPFIHNAFK TDIQICILDG EMMAYNPNTQ TFMQKGTKFD 350
    IKRMVEDSDL QTCYCVFDVL MVNNKKLGHE TLRKRYEILS SIFTPIPGRI 400
    EIVQKTQAHT KNEVIDALNE AIDKREEGIM IKQPLSIYKP DKRGEGWLKI 450
    KPEYVSGLMD ELDILIVGGY WGKGSRGGMM SHFLCAVAEK PPPGEKPSVF 500
    HTLSRVGSGC TMKELYDLGL KLAKYWKPFH KKAPPSSILC GTEKPEVYIE 550
    PCNSVIVQIK AAEIVPSDMY KTGCTLRFPR IEKIRDDKEW HECMTLDDLE 600
    QLRGKASGKL ASKHFYVGGD DEPQEKKRKA APKMKKVIGI IEHLKAPNLT 650
    NVNKISNIFE DVEFCVMSGT DSQPKPDLEN RIAEFGGYIV QNPGPDTYCV 700
    IAGSKNIRVK NIILSNKHDV VKPAWLLECF KTKSFVPWQP HFMIHMCPST 750
    KEHFAREYDC YGDSYFVDTD LNQLKEVFSG IKNSNEQTPE EMASLIADLE 800
    YRYSWDCSPL SMFRRHTVYL DLYAVINDLS TKNEGTRLAI KALELRFHGA 850
    KVVSCLAEGV SHVIIGEDHS RIADFKAFRR TFKRKFKILK ESWITDSIDK 900
    CELQEENQYL I 911
    Length:911
    Mass (Da):104,053
    Last modified:December 21, 2004 - v1
    Checksum:iC6AD9817E9EC2B59
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CR860475 mRNA. Translation: CAH92597.1.
    RefSeqiNP_001126522.1. NM_001133050.1.

    Genome annotation databases

    GeneIDi100173511.
    KEGGipon:100173511.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    CR860475 mRNA. Translation: CAH92597.1 .
    RefSeqi NP_001126522.1. NM_001133050.1.

    3D structure databases

    ProteinModelPortali Q5R6L3.
    SMRi Q5R6L3. Positions 654-759.
    ModBasei Search...
    MobiDBi Search...

    Proteomic databases

    PRIDEi Q5R6L3.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    GeneIDi 100173511.
    KEGGi pon:100173511.

    Organism-specific databases

    CTDi 3981.

    Phylogenomic databases

    HOVERGENi HBG005516.
    InParanoidi Q5R6L3.
    KOi K10777.

    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.
    IPR016059. DNA_ligase_ATP-dep_CS.
    IPR012308. DNA_ligase_ATP-dep_N.
    IPR021536. DNA_ligase_IV_dom.
    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.
    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.
    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 German cDNA consortium
      Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
      Tissue: Brain cortex.

    Entry informationi

    Entry nameiDNLI4_PONAB
    AccessioniPrimary (citable) accession number: Q5R6L3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: February 7, 2006
    Last sequence update: December 21, 2004
    Last modified: October 1, 2014
    This is version 55 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programChordata Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3