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Q08387

- DNLI4_YEAST

UniProt

Q08387 - DNLI4_YEAST

Protein

DNA ligase 4

Gene

DNL4

Organism
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 128 (01 Oct 2014)
      Sequence version 1 (01 Nov 1996)
      Previous versions | rss
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    Functioni

    Has minor DNA joining activity. Can act on oligo(PDT)/poly(rA) substrate.

    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 sitei280 – 2801ATPBy similarity
    Active sitei282 – 2821N6-AMP-lysine intermediatePROSITE-ProRule annotation
    Binding sitei287 – 2871ATPBy similarity
    Binding sitei304 – 3041ATPBy similarity
    Metal bindingi340 – 3401Magnesium 1Sequence Analysis
    Metal bindingi442 – 4421Magnesium 2Sequence Analysis
    Binding sitei447 – 4471ATPBy similarity
    Binding sitei458 – 4581ATPBy similarity
    Binding sitei464 – 4641ATPBy similarity

    GO - Molecular functioni

    1. ATP binding Source: UniProtKB-KW
    2. DNA binding Source: InterPro
    3. DNA ligase (ATP) activity Source: SGD
    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
    6. double-strand break repair via nonhomologous end joining Source: SGD
    7. replicative cell aging Source: SGD

    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

    Enzyme and pathway databases

    BioCyciYEAST:G3O-33555-MONOMER.
    BRENDAi6.5.1.1. 984.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    DNA ligase 4 (EC:6.5.1.1)
    Alternative name(s):
    DNA ligase II
    DNA ligase IV
    Polydeoxyribonucleotide synthase [ATP] 4
    Gene namesi
    Name:DNL4
    Synonyms:LIG4
    Ordered Locus Names:YOR005C
    ORF Names:UND407, UNE452
    OrganismiSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
    Taxonomic identifieri559292 [NCBI]
    Taxonomic lineageiEukaryotaFungiDikaryaAscomycotaSaccharomycotinaSaccharomycetesSaccharomycetalesSaccharomycetaceaeSaccharomyces
    ProteomesiUP000002311: Chromosome XV

    Organism-specific databases

    CYGDiYOR005c.
    SGDiS000005531. DNL4.

    Subcellular locationi

    Nucleus Curated

    GO - Cellular componenti

    1. DNA ligase IV complex Source: SGD

    Keywords - Cellular componenti

    Nucleus

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 944944DNA ligase 4PRO_0000059582Add
    BLAST

    Proteomic databases

    PaxDbiQ08387.

    Expressioni

    Gene expression databases

    GenevestigatoriQ08387.

    Interactioni

    Subunit structurei

    Interacts with LIF1 via its BRCT domain. Interacts with POL4 in the DNL4-LIF1 complex.3 Publications

    Protein-protein interaction databases

    BioGridi34408. 49 interactions.
    DIPiDIP-5801N.
    IntActiQ08387. 1 interaction.
    MINTiMINT-672762.
    STRINGi4932.YOR005C.

    Structurei

    Secondary structure

    1
    944
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi694 – 6985
    Beta strandi704 – 7074
    Helixi712 – 7198
    Beta strandi737 – 7404
    Helixi745 – 7506
    Turni751 – 7544
    Helixi764 – 7674
    Turni784 – 7874
    Helixi788 – 7914
    Helixi792 – 7943
    Beta strandi797 – 7993
    Beta strandi801 – 8044
    Helixi808 – 8136
    Helixi861 – 8677
    Beta strandi875 – 8773
    Beta strandi879 – 8824
    Turni888 – 8903
    Helixi891 – 8944
    Helixi897 – 9004
    Turni901 – 9077
    Beta strandi908 – 9114
    Beta strandi917 – 9193
    Helixi922 – 9287

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1Z56X-ray3.92C681-943[»]
    ProteinModelPortaliQ08387.
    SMRiQ08387. Positions 43-599, 683-939.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ08387.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini681 – 780100BRCT 1PROSITE-ProRule annotationAdd
    BLAST
    Domaini836 – 941106BRCT 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

    eggNOGiCOG1793.
    GeneTreeiENSGT00750000117695.
    HOGENOMiHOG000093622.
    KOiK10777.
    OMAiISHFLCA.
    OrthoDBiEOG7QC84G.

    Family and domain databases

    Gene3Di2.40.50.140. 1 hit.
    InterProiIPR001357. BRCT_dom.
    IPR000977. DNA_ligase_ATP-dep.
    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.
    PF01068. DNA_ligase_A_M. 1 hit.
    PF04675. DNA_ligase_A_N. 1 hit.
    [Graphical view]
    SMARTiSM00292. BRCT. 1 hit.
    [Graphical view]
    SUPFAMiSSF50249. SSF50249. 2 hits.
    SSF52113. SSF52113. 3 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.

    Q08387-1 [UniParc]FASTAAdd to Basket

    « Hide

    MISALDSIPE PQNFAPSPDF KWLCEELFVK IHEVQINGTA GTGKSRSFKY    50
    YEIISNFVEM WRKTVGNNIY PALVLALPYR DRRIYNIKDY VLIRTICSYL 100
    KLPKNSATEQ RLKDWKQRVG KGGNLSSLLV EEIAKRRAEP SSKAITIDNV 150
    NHYLDSLSGD RFASGRGFKS LVKSKPFLHC VENMSFVELK YFFDIVLKNR 200
    VIGGQEHKLL NCWHPDAQDY LSVISDLKVV TSKLYDPKVR LKDDDLSIKV 250
    GFAFAPQLAK KVNLSYEKIC RTLHDDFLVE EKMDGERIQV HYMNYGESIK 300
    FFSRRGIDYT YLYGASLSSG TISQHLRFTD SVKECVLDGE MVTFDAKRRV 350
    ILPFGLVKGS AKEALSFNSI NNVDFHPLYM VFDLLYLNGT SLTPLPLHQR 400
    KQYLNSILSP LKNIVEIVRS SRCYGVESIK KSLEVAISLG SEGVVLKYYN 450
    SSYNVASRNN NWIKVKPEYL EEFGENLDLI VIGRDSGKKD SFMLGLLVLD 500
    EEEYKKHQGD SSEIVDHSSQ EKHIQNSRRR VKKILSFCSI ANGISQEEFK 550
    EIDRKTRGHW KRTSEVAPPA SILEFGSKIP AEWIDPSESI VLEIKSRSLD 600
    NTETNMQKYA TNCTLYGGYC KRIRYDKEWT DCYTLNDLYE SRTVKSNPSY 650
    QAERSQLGLI RKKRKRVLIS DSFHQNRKQL PISNIFAGLL FYVLSDYVTE 700
    DTGIRITRAE LEKTIVEHGG KLIYNVILKR HSIGDVRLIS CKTTTECKAL 750
    IDRGYDILHP NWVLDCIAYK RLILIEPNYC FNVSQKMRAV AEKRVDCLGD 800
    SFENDISETK LSSLYKSQLS LPPMGELEID SEVRRFPLFL FSNRIAYVPR 850
    RKISTEDDII EMKIKLFGGK ITDQQSLCNL IIIPYTDPIL RKDCMNEVHE 900
    KIKEQIKASD TIPKIARVVA PEWVDHSINE NCQVPEEDFP VVNY 944
    Length:944
    Mass (Da):108,515
    Last modified:November 1, 1996 - v1
    Checksum:i7FB6D7927E1719B5
    GO

    Sequence cautioni

    The sequence AAC49484.1 differs from that shown. Reason: Frameshift at positions 408 and 413. Produces 2 separate ORFs.
    The sequence AAC49485.1 differs from that shown. Reason: Frameshift at positions 408 and 413. Produces 2 separate ORFs.

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U43491 Genomic DNA. Translation: AAC49485.1. Frameshift.
    U43491 Genomic DNA. Translation: AAC49484.1. Frameshift.
    Z74913 Genomic DNA. Translation: CAA99193.1.
    BK006948 Genomic DNA. Translation: DAA10787.1.
    PIRiS66870.
    RefSeqiNP_014647.1. NM_001183424.1.

    Genome annotation databases

    EnsemblFungiiYOR005C; YOR005C; YOR005C.
    GeneIDi854166.
    KEGGisce:YOR005C.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    U43491 Genomic DNA. Translation: AAC49485.1 . Frameshift.
    U43491 Genomic DNA. Translation: AAC49484.1 . Frameshift.
    Z74913 Genomic DNA. Translation: CAA99193.1 .
    BK006948 Genomic DNA. Translation: DAA10787.1 .
    PIRi S66870.
    RefSeqi NP_014647.1. NM_001183424.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1Z56 X-ray 3.92 C 681-943 [» ]
    ProteinModelPortali Q08387.
    SMRi Q08387. Positions 43-599, 683-939.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    BioGridi 34408. 49 interactions.
    DIPi DIP-5801N.
    IntActi Q08387. 1 interaction.
    MINTi MINT-672762.
    STRINGi 4932.YOR005C.

    Proteomic databases

    PaxDbi Q08387.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblFungii YOR005C ; YOR005C ; YOR005C .
    GeneIDi 854166.
    KEGGi sce:YOR005C.

    Organism-specific databases

    CYGDi YOR005c.
    SGDi S000005531. DNL4.

    Phylogenomic databases

    eggNOGi COG1793.
    GeneTreei ENSGT00750000117695.
    HOGENOMi HOG000093622.
    KOi K10777.
    OMAi ISHFLCA.
    OrthoDBi EOG7QC84G.

    Enzyme and pathway databases

    BioCyci YEAST:G3O-33555-MONOMER.
    BRENDAi 6.5.1.1. 984.

    Miscellaneous databases

    EvolutionaryTracei Q08387.
    NextBioi 975950.
    PROi Q08387.

    Gene expression databases

    Genevestigatori Q08387.

    Family and domain databases

    Gene3Di 2.40.50.140. 1 hit.
    InterProi IPR001357. BRCT_dom.
    IPR000977. DNA_ligase_ATP-dep.
    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.
    PF01068. DNA_ligase_A_M. 1 hit.
    PF04675. DNA_ligase_A_N. 1 hit.
    [Graphical view ]
    SMARTi SM00292. BRCT. 1 hit.
    [Graphical view ]
    SUPFAMi SSF50249. SSF50249. 2 hits.
    SSF52113. SSF52113. 3 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 sequence of a 30 kb fragment on the left arm of chromosome XV from Saccharomyces cerevisiae reveals 15 open reading frames, five of which correspond to previously identified genes."
      Sterky F., Holmberg A., Pettersson B., Uhlen M.
      Yeast 12:1091-1095(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    2. "The nucleotide sequence of Saccharomyces cerevisiae chromosome XV."
      Dujon B., Albermann K., Aldea M., Alexandraki D., Ansorge W., Arino J., Benes V., Bohn C., Bolotin-Fukuhara M., Bordonne R., Boyer J., Camasses A., Casamayor A., Casas C., Cheret G., Cziepluch C., Daignan-Fornier B., Dang V.-D.
      , de Haan M., Delius H., Durand P., Fairhead C., Feldmann H., Gaillon L., Galisson F., Gamo F.-J., Gancedo C., Goffeau A., Goulding S.E., Grivell L.A., Habbig B., Hand N.J., Hani J., Hattenhorst U., Hebling U., Hernando Y., Herrero E., Heumann K., Hiesel R., Hilger F., Hofmann B., Hollenberg C.P., Hughes B., Jauniaux J.-C., Kalogeropoulos A., Katsoulou C., Kordes E., Lafuente M.J., Landt O., Louis E.J., Maarse A.C., Madania A., Mannhaupt G., Marck C., Martin R.P., Mewes H.-W., Michaux G., Paces V., Parle-McDermott A.G., Pearson B.M., Perrin A., Pettersson B., Poch O., Pohl T.M., Poirey R., Portetelle D., Pujol A., Purnelle B., Ramezani Rad M., Rechmann S., Schwager C., Schweizer M., Sor F., Sterky F., Tarassov I.A., Teodoru C., Tettelin H., Thierry A., Tobiasch E., Tzermia M., Uhlen M., Unseld M., Valens M., Vandenbol M., Vetter I., Vlcek C., Voet M., Volckaert G., Voss H., Wambutt R., Wedler H., Wiemann S., Winsor B., Wolfe K.H., Zollner A., Zumstein E., Kleine K.
      Nature 387:98-102(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 204508 / S288c.
    3. Cited for: GENOME REANNOTATION.
      Strain: ATCC 204508 / S288c.
    4. "Two distinct DNA ligase activities in mitotic extracts of the yeast Saccharomyces cerevisiae."
      Ramos W., Tappe N., Talamantez J., Friedberg E.C., Tomkinson A.E.
      Nucleic Acids Res. 25:1485-1492(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
    5. "Saccharomyces cerevisiae LIF1: a function involved in DNA double-strand break repair related to mammalian XRCC4."
      Herrmann G., Lindahl T., Schar P.
      EMBO J. 17:4188-4198(1998) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH LIF1.
    6. "A physical and functional interaction between yeast Pol4 and Dnl4-Lif1 links DNA synthesis and ligation in nonhomologous end joining."
      Tseng H.-M., Tomkinson A.E.
      J. Biol. Chem. 277:45630-45637(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: INTERACTION WITH POL4.
    7. "Structure of an Xrcc4-DNA ligase IV yeast ortholog complex reveals a novel BRCT interaction mode."
      Dore A.S., Furnham N., Davies O.R., Sibanda B.L., Chirgadze D.Y., Jackson S.P., Pellegrini L., Blundell T.L.
      DNA Repair 5:362-368(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (3.92 ANGSTROMS) OF 681-944 IN COMPLEX WITH LIF1.

    Entry informationi

    Entry nameiDNLI4_YEAST
    AccessioniPrimary (citable) accession number: Q08387
    Secondary accession number(s): D6W271, Q02913, Q02914
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: November 1, 1997
    Last sequence update: November 1, 1996
    Last modified: October 1, 2014
    This is version 128 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programFungal Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families
    3. Yeast
      Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD
    4. Yeast chromosome XV
      Yeast (Saccharomyces cerevisiae) chromosome XV: entries and gene names

    External Data

    Dasty 3