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Protein Overview: RAD3

General Information:
Name(s) found: RAD3 / YER171W [SGD]
Description(s) found:
Found 32 descriptions.
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  • 5' to 3' DNA helicase, involved in nucleotide excision repair and transcription; subunit of RNA polymerase II transcription initiation factor TFIIH; subunit of Nucleotide Excision Repair Factor 3 (NEF3); homolog of human XPD protein [SGD]
    • Organism: Saccharomyces cerevisiae
    Length: 778 amino acids

    Gene Ontology:
    Cellular Component: holo TFIIH complex [IDALink to PubMed articleLink to PubMed article]
    nucleotide-excision repair factor 3 complex [IDALink to PubMed article]
    Biological Process: negative regulation of transcription from RNA polymerase II promoter, mitotic [TASLink to PubMed article]
    nucleotide-excision repair, DNA duplex unwinding [TASLink to PubMed article]
    nucleotide-excision repair [IDALink to PubMed article]
    transcription initiation from RNA polymerase II promoter [TASLink to PubMed articleLink to PubMed article]
    Molecular Function: DNA helicase activity [TASLink to PubMed article]
    general RNA polymerase II transcription factor activity [TASLink to PubMed article]


    Sequence:
    Sequence:
    [PDR BLAST]
    [ProtParam] 
          1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MKFYIDDLPV LFPYPKIYPE QYNYMCDIKK TLDVGGNSIL EMPSGTGKTV SLLSLTIAYQ  60
   61 MHYPEHRKII YCSRTMSEIE KALVELENLM DYRTKELGYQ EDFRGLGLTS RKNLCLHPEV 120
  121 SKERKGTVVD EKCRRMTNGQ AKRKLEEDPE ANVELCEYHE NLYNIEVEDY LPKGVFSFEK 180
  181 LLKYCEEKTL CPYFIVRRMI SLCNIIIYSY HYLLDPKIAE RVSNEVSKDS IVIFDEAHNI 240
  241 DNVCIESLSL DLTTDALRRA TRGANALDER ISEVRKVDSQ KLQDEYEKLV QGLHSADILT 300
  301 DQEEPFVETP VLPQDLLTEA IPGNIRRAEH FVSFLKRLIE YLKTRMKVLH VISETPKSFL 360
  361 QHLKQLTFIE RKPLRFCSER LSLLVRTLEV TEVEDFTALK DIATFATLIS TYEEGFLLII 420
  421 EPYEIENAAV PNPIMRFTCL DASIAIKPVF ERFSSVIITS GTISPLDMYP RMLNFKTVLQ 480
  481 KSYAMTLAKK SFLPMIITKG SDQVAISSRF EIRNDPSIVR NYGSMLVEFA KITPDGMVVF 540
  541 FPSYLYMESI VSMWQTMGIL DEVWKHKLIL VETPDAQETS LALETYRKAC SNGRGAILLS 600
  601 VARGKVSEGI DFDHQYGRTV LMIGIPFQYT ESRILKARLE FMRENYRIRE NDFLSFDAMR 660
  661 HAAQCLGRVL RGKDDYGVMV LADRRFSRKR SQLPKWIAQG LSDADLNLST DMAISNTKQF 720
  721 LRTMAQPTDP KDQEGVSVWS YEDLIKHQNS RKDQGGFIEN ENKEGEQDED EDEDIEMQ

    Protein Complex Data

      PUBLICATION TOPOLOGY COCOMPLEXED PROTEINS
    View Details Riffle et al. (2010) (Unpublished Data) MET18 RAD3 TFB3
    View Details (MIPS) Mewes HW, et al. (2004) CCL1 KIN28 RAD2 RAD3 SSL1 SSL2 TFB1 TFB2 TFB3 TFB4
    View Details Krogan NJ, et al. (2006) CCL1 ESP1 KIN28 RAD3 SSL1 TFB1 TFB3 TFB4
    View Details Gavin AC, et al. (2006) MET18 RAD3
    View Details Gavin AC, et al. (2002) ASC1 CLU1 ECM29 GCN1 GCN20 MET18 RAD3 RPN10 RPT3 RPT6 TFP1 TUB3 YDJ1
    View Details Ho Y, et al. (2002) AAC1 AAC3 ACH1 ACO1 ADH4 ADH6 ATP3 BCY1 BIO3 CCL1 CDC33 ECM10 ERG20 GDI1 HOR2 HXT6 IDH2 KIN28 LSC1 MAM33 MDH1 MET18 PRB1 PTC7 QCR2 RAD26 RAD3 RHR2 RPN1 RPN8 RPT3 SEC53 TEF4 TFB3 TFP1 THI22 TIF1, TIF2 TMA29 YBR184W YSP2
    View Details Qiu et al. (2008) CCL1 ELC1 KIN28 RAD2 RAD3 SSL1 SSL2 TFB1 TFB2 TFB3 TFB4 TFB5

    Mass Spectrometry Data

    The following runs contain data for this protein:

      BAIT COMMENTS PUBLICATION
    View Run RPA135 No Comments Schneider, DA, et al. (2006)
    View Run MLP2 #21 Asynchronous Prep2-IMAC Phosphopeptide enrichment A1 Keck JM, et al. (2011)
    View Run MLP2 #03 Alpha Factor Prep1-TiO2 Flowthrough Keck JM, et al. (2011)

    Yeast Two-Hybrid Data

    The following interactions contain this protein:

    SHOWING SINGLE HITS. [ Hide Single Hits ]

    [View our yeast two-hybrid interpretation guidelines.]

      BAIT PREY HITS PUBLICATION
    View Screen CHK1 RAD3 2 Unpublished Fields Lab Data
    View Screen CAB2 RAD3 1 Unpublished Fields Lab Data
    View Screen UBC7 RAD3 1 Unpublished Fields Lab Data

    Microscopy / Localization Data

    New Feature: Upload Your Own Microscopy Data

      PROTEIN(S) PUBLICATION
    View Data RAD3 Huh WK, et al. (2003)

    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..221] PSI-BLAST 39.0 Putative DEAD box RNA helicase
    2 View Details [222..389] PSI-BLAST 39.0 Putative DEAD box RNA helicase
    3 View Details [390..441] deduced N/A No confident structure predictions are available.
    4 View Details [442..725] ORFEUS 9.08 Initiation factor 4a
    5 View Details [726..778] deduced N/A No confident structure predictions are available.

    Functions predicted (by domain):

    # Gene Ontology predictions
    1
    Term Confidence Notes
  • general RNA polymerase II transcription factor activity
    		•  5.47805400577115 bayes_pls_golite062009
  • dATP binding
    		•  3.90236137621968 bayes_pls_golite062009
  • adenyl deoxyribonucleotide binding
    		•  2.90098016780049 bayes_pls_golite062009
  • purine deoxyribonucleotide binding
    		•  2.90098016780049 bayes_pls_golite062009
  • DNA-dependent ATPase activity
    		•  2.72462789867829 bayes_pls_golite062009
  • deoxyribonuclease activity
    		•  2.72222787956584 bayes_pls_golite062009
  • binding
    		•  2.64537357529343 bayes_pls_golite062009
  • endodeoxyribonuclease activity
    		•  2.60873257753475 bayes_pls_golite062009
  • hydrolase activity
    		•  2.55157966585974 bayes_pls_golite062009
  • nucleic acid binding
    		•  2.51683451033161 bayes_pls_golite062009
  • DNA helicase activity
    		•  2.2817164193758 bayes_pls_golite062009
  • pyrophosphatase activity
    		•  2.13284212711072 bayes_pls_golite062009
  • DNA binding
    		•  2.12258000781149 bayes_pls_golite062009
  • transcription regulator activity
    		•  2.09345198747025 bayes_pls_golite062009
  • endonuclease activity
    		•  1.96689197136388 bayes_pls_golite062009
  • ATP-dependent DNA helicase activity
    		•  1.88455339138556 bayes_pls_golite062009
  • helicase activity
    		•  1.70242731830224 bayes_pls_golite062009
  • microtubule motor activity
    		•  1.6537049553461 bayes_pls_golite062009
  • RNA helicase activity
    		•  1.63960194106079 bayes_pls_golite062009
  • ATP-dependent RNA helicase activity
    		•  1.61735400124552 bayes_pls_golite062009
  • RNA-dependent ATPase activity
    		•  1.60404584546501 bayes_pls_golite062009
  • protein-DNA loading ATPase activity
    		•  1.29640539057136 bayes_pls_golite062009
  • structure-specific DNA binding
    		•  1.2539059700735 bayes_pls_golite062009
  • protein binding
    		•  1.22129154759482 bayes_pls_golite062009
  • purine NTP-dependent helicase activity
    		•  1.19311444180077 bayes_pls_golite062009
  • ATP-dependent helicase activity
    		•  1.19311444180077 bayes_pls_golite062009
  • motor activity
    		•  1.14667913749579 bayes_pls_golite062009
  • DNA clamp loader activity
    		•  1.12431517057397 bayes_pls_golite062009
  • double-stranded DNA binding
    		•  1.117585097627 bayes_pls_golite062009
  • transcription elongation regulator activity
    		•  1.11383295816593 bayes_pls_golite062009
  • catalytic activity
    		•  1.00104173493322 bayes_pls_golite062009
  • transcription activator activity
    		•  0.889929694023098 bayes_pls_golite062009
  • transcription factor activity
    		•  0.887108427603557 bayes_pls_golite062009
  • ion transmembrane transporter activity
    		•  0.595694294246159 bayes_pls_golite062009
  • single-stranded DNA binding
    		•  0.568457189190858 bayes_pls_golite062009
  • sequence-specific DNA binding
    		•  0.543891899378373 bayes_pls_golite062009
  • cytoskeletal protein binding
    		•  0.500462538667228 bayes_pls_golite062009
  • cation transmembrane transporter activity
    		•  0.394186699348086 bayes_pls_golite062009
  • purine nucleotide binding
    		•  0.360529478474946 bayes_pls_golite062009
  • nucleotide binding
    		•  0.354857598792381 bayes_pls_golite062009
  • purine ribonucleotide binding
    		•  0.35235724478784 bayes_pls_golite062009
  • ribonucleotide binding
    		•  0.352298062690593 bayes_pls_golite062009
  • mismatched DNA binding
    		•  0.31144582840038 bayes_pls_golite062009
  • DNA strand annealing activity
    		•  0.283577486331079 bayes_pls_golite062009
  • four-way junction helicase activity
    		•  0.26252931460003 bayes_pls_golite062009
  • RNA polymerase II transcription factor activity
    		•  0.243902356228423 bayes_pls_golite062009
  • exodeoxyribonuclease V activity
    		•  0.185603938981231 bayes_pls_golite062009
  • nucleotidyltransferase activity
    		•  0.181509771587324 bayes_pls_golite062009
  • nucleoside-triphosphatase activity
    		•  0.147579541298736 bayes_pls_golite062009
  • hydrolase activity, acting on acid anhydrides
    		•  0.113504049290503 bayes_pls_golite062009
  • hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides
    		•  0.111293884322157 bayes_pls_golite062009
  • structural constituent of ribosome
    		•  0.089234257580272 bayes_pls_golite062009
  • actin binding
    		•  0.00482938540552702 bayes_pls_golite062009
    2 No functions predicted.
    3 No functions predicted.
    4 No functions predicted.
    5 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: 0.97

    Source: Reynolds et al. (2008)

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