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Protein Overview: DNL4

General Information:
Name(s) found: DNL4 / YOR005C [SGD]
Description(s) found:
Found 27 descriptions.
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  • DNA ligase required for nonhomologous end-joining (NHEJ), forms stable heterodimer with required cofactor Lif1p, interacts with Nej1p; involved in meiosis, not essential for vegetative growth [SGD]
    • Organism: Saccharomyces cerevisiae
    Length: 944 amino acids

    Gene Ontology:
    Cellular Component: nucleus [TASLink to PubMed article]
    Biological Process: double-strand break repair via nonhomologous end joining [IDALink to PubMed article][IMPLink to PubMed article]
    Molecular Function: DNA ligase (ATP) activity [IDALink to PubMed article]


    Sequence:
    Sequence:
    [PDR BLAST]
    [ProtParam] 
          1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MISALDSIPE PQNFAPSPDF KWLCEELFVK IHEVQINGTA GTGKSRSFKY YEIISNFVEM  60
   61 WRKTVGNNIY PALVLALPYR DRRIYNIKDY VLIRTICSYL KLPKNSATEQ RLKDWKQRVG 120
  121 KGGNLSSLLV EEIAKRRAEP SSKAITIDNV NHYLDSLSGD RFASGRGFKS LVKSKPFLHC 180
  181 VENMSFVELK YFFDIVLKNR VIGGQEHKLL NCWHPDAQDY LSVISDLKVV TSKLYDPKVR 240
  241 LKDDDLSIKV GFAFAPQLAK KVNLSYEKIC RTLHDDFLVE EKMDGERIQV HYMNYGESIK 300
  301 FFSRRGIDYT YLYGASLSSG TISQHLRFTD SVKECVLDGE MVTFDAKRRV ILPFGLVKGS 360
  361 AKEALSFNSI NNVDFHPLYM VFDLLYLNGT SLTPLPLHQR KQYLNSILSP LKNIVEIVRS 420
  421 SRCYGVESIK KSLEVAISLG SEGVVLKYYN SSYNVASRNN NWIKVKPEYL EEFGENLDLI 480
  481 VIGRDSGKKD SFMLGLLVLD EEEYKKHQGD SSEIVDHSSQ EKHIQNSRRR VKKILSFCSI 540
  541 ANGISQEEFK EIDRKTRGHW KRTSEVAPPA SILEFGSKIP AEWIDPSESI VLEIKSRSLD 600
  601 NTETNMQKYA TNCTLYGGYC KRIRYDKEWT DCYTLNDLYE SRTVKSNPSY QAERSQLGLI 660
  661 RKKRKRVLIS DSFHQNRKQL PISNIFAGLL FYVLSDYVTE DTGIRITRAE LEKTIVEHGG 720
  721 KLIYNVILKR HSIGDVRLIS CKTTTECKAL IDRGYDILHP NWVLDCIAYK RLILIEPNYC 780
  781 FNVSQKMRAV AEKRVDCLGD SFENDISETK LSSLYKSQLS LPPMGELEID SEVRRFPLFL 840
  841 FSNRIAYVPR RKISTEDDII EMKIKLFGGK ITDQQSLCNL IIIPYTDPIL RKDCMNEVHE 900
  901 KIKEQIKASD TIPKIARVVA PEWVDHSINE NCQVPEEDFP VVNY

    Protein Complex Data

      PUBLICATION TOPOLOGY COCOMPLEXED PROTEINS
    View Details (MIPS) Mewes HW, et al. (2004) DNL4 LIF1
    View Details Ho Y, et al. (2002) ACO1 AHP1 CIC1 DNL4 GDE1 HTA1 KGD1 LIF1 MAK16 MEC3 NOP15 NOP2 NOP7 NSA1 RKM2 RPF2 RRT6 TIF6 YTM1

    Mass Spectrometry Data

    The following runs contain data for this protein:

      BAIT COMMENTS PUBLICATION
    View Run MLP2 #12 Mitotic Prep1-TiO2 Flowthrough Keck JM, et al. (2011)
    View Run MLP2 #10 Mitotic Prep1-TiO2 Phosphopeptide enrichment Keck JM, et al. (2011)
    View Run MLP2 #11 Mitotic Prep1-TiO2 enriched, new search criteria Keck JM, et al. (2011)

    Yeast Two-Hybrid Data

    The following interactions contain this protein:

    NOT SHOWING SINGLE HITS. [ Show Single Hits ]

    [View our yeast two-hybrid interpretation guidelines.]

    No yeast two-hybrid interactions found for this protein.

    Microscopy / Localization Data

    New Feature: Upload Your Own Microscopy Data

    No microscopy data found in the PDR for this protein.

    Protein Structure Data


    [What does the above image mean?]
    [View Top Sequence Alignments] [Show Ginzu Version Information]

    Domains predicted:

    #   Region(s) Method Confidence Match Description
    1 View Details [1..242] MSA 1.096977 View MSA. No confident structure predictions are available.
    2 View Details [243..309] ORFEUS 8.04 ATP-dependent DNA ligase; ATP-dependent DNA ligase, N-terminal domain
    3 View Details [310..421] PSI-BLAST 26.30103 ATP-dependent DNA ligase; ATP-dependent DNA ligase, N-terminal domain
    4 View Details [422..468] PSI-BLAST 26.30103 ATP-dependent DNA ligase; ATP-dependent DNA ligase, N-terminal domain
    5 View Details [469..579] PSI-BLAST 26.30103 ATP-dependent DNA ligase; ATP-dependent DNA ligase, N-terminal domain
    6 View Details [580..733] deduced N/A No confident structure predictions are available.
    7 View Details [734..816] PSI-BLAST 5.39794 CRYSTAL STRUCTURE OF A XRCC4-DNA LIGASE IV COMPLEX
    8 View Details [817..944] deduced N/A No confident structure predictions are available.

    Functions predicted (by domain):

    # Gene Ontology predictions
    1
    Term Confidence Notes
  • DNA ligase activity
    		•  10.0279903057926 bayes_pls_golite062009
  • ligase activity, forming phosphoric ester bonds
    		•  9.92846900587219 bayes_pls_golite062009
  • DNA ligase (ATP) activity
    		•  8.51283882444113 bayes_pls_golite062009
  • DNA ligase (NAD+) activity
    		•  3.17397926295565 bayes_pls_golite062009
  • ligase activity
    		•  2.36807839237461 bayes_pls_golite062009
  • catalytic activity
    		•  2.15370807854636 bayes_pls_golite062009
  • binding
    		•  1.82998145778732 bayes_pls_golite062009
  • protein binding
    		•  1.38006517521813 bayes_pls_golite062009
  • nucleic acid binding
    		•  1.06318697852063 bayes_pls_golite062009
  • DNA binding
    		•  0.920391596538289 bayes_pls_golite062009
    2 No functions predicted.
    3 No functions predicted.
    4 No functions predicted.
    5 No functions predicted.
    6 No functions predicted.
    7 No functions predicted.
    8 No functions predicted.


    Reference: Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076


    Philius Transmembrane Prediction:

    Protein predicted to be: GLOBULAR (No transmembrane regions or signal peptide)
    Confidence of classification: 0.98

    Source: Reynolds et al. (2008)

    YRC Informatics Platform - Version 3.0
    Created and Maintained by: Michael Riffle