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Protein Overview: NRD1

General Information:
Name(s) found: NRD1 / YNL251C [SGD]
Description(s) found:
Found 30 descriptions.
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  • RNA-binding protein that interacts with the C-terminal domain of the RNA polymerase II large subunit (Rpo21p), preferentially at phosphorylated Ser5; required for transcription termination and 3' end maturation of nonpolyadenylated RNAs [SGD]
    • Organism: Saccharomyces cerevisiae
    Length: 575 amino acids

    Gene Ontology:
    Cellular Component: nuclear exosome (RNase complex) [IPILink to PubMed article]
    nucleus [IPILink to PubMed article]
    Biological Process: termination of RNA polymerase II transcription, poly(A)-independent [IGILink to PubMed article][IMPLink to PubMed articleLink to PubMed article][IPILink to PubMed article]
    Molecular Function: RNA binding [IDALink to PubMed article]


    Sequence:
    Sequence:
    [PDR BLAST]
    [ProtParam] 
          1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MQQDDDFQNF VATLESFKDL KSGISGSRIK KLTTYALDHI DIESKIISLI IDYSRLCPDS  60
   61 HKLGSLYIID SIGRAYLDET RSNSNSSSNK PGTCAHAINT LGEVIQELLS DAIAKSNQDH 120
  121 KEKIRMLLDI WDRSGLFQKS YLNAIRSKCF AMDISNNTAN TASQQLSLDP KQRSKQILSN 180
  181 LKKSPPLNLN ISLPTDLTST DPAKQQAALF QVIAALQKHF KTLPSHTSVG TVAPPQAHTI 240
  241 TEYGSRRERE RERERYNSRR NRSRSPPAPF SQPSTGRKDR YPSVAQDQYS IGAPNTTFGT 300
  301 NNHHLYPDEL NVSNNPHYRP KPVSYDSTLP PDHIKVYSRT LFIGGVPLNM KEWDLANVLK 360
  361 PFAEVQSVIL NNSRKHAFVK VYSRHEAENV LQNFNKDGAL PLRTRWGVGF GPRDCCDYQH 420
  421 GYSIIPMHRL TDADKKWSVS AQWGGTSGQP LVTGIVFEEP DIIVGEGVSS KAISQKMPTD 480
  481 SGRNGPRSGK PNKSGSISSI SPVPYGNAPL ASPPPQQYVQ PMMQQPYGYA PNQPLPSQGP 540
  541 AAAAPPVPQQ QFDPTAQLNS LMNMLNQQQQ QQQQS

    Protein Complex Data

      PUBLICATION TOPOLOGY COCOMPLEXED PROTEINS
    View Details Riffle et al. (2010) (Unpublished Data) CBC2 KEM1 NAB3 NAB6 NRD1 SEN1 STO1 TIF4632
    View Details Krogan NJ, et al. (2006) GAT1 NAB3 NRD1
    View Details Gavin AC, et al. (2006) MTR4 NAB3 NRD1 SEN1 STO1
    View Details Gavin AC, et al. (2002) ABF2 AIR2 BRR1 BUR2 CBC2 CKA1 CKA2 CKB1 CKB2 CLU1 CRN1 CTI6 DEP1 DOT6 EAF3 ECM16 ECM29 HCA4 HTA1 HTA2 IML1 IOC3 ISW1 KAP123 KAP95 LHP1 LUC7 MEC1 MED4 MIP6 MIS1 MRPL23 MSH4 MUD1 NAB3 NAB6 NAM7 NAM8 NHP10 NPL3 NRD1 NRP1 NUP60 PHO23 POL2 PRP39 PRP40 PRP42 PUB1 RCO1 ROM2 RPA135 RPD3 RSC8 RSE1 RXT2 RXT3 SAP30 SCP160 SDS3 SEN1 SEN54 SGN1 SGV1 SIN3 SMD1 SMD2 SMD3 SNF2 SNP1 SNU56 SNU71 SRO9 SRP1 STO1 SUI3 SUP35 SUP45 SWI1 TAO3 THO2 TIF4631 TIF4632 TOP1 TUP1 UME1 UME6 USO1 UTP20 VAC14 VPS1 VPS5 YJL017W YRA2

    Mass Spectrometry Data

    The following runs contain data for this protein:

      BAIT COMMENTS PUBLICATION
    View Run RPA135 his-HA tag on RPA135 Schneider, DA, et al. (2006)
    View Run ZDS1 Sample 3 - cpn + atp, from june 2005 McCusker D, et al (2007)
    View Run MLP2 #19 Asynchronous Prep1-TiO2 Phosphopeptide enrichment Keck JM, et al. (2011)
    View Run MLP2 #19b Asynchronous Prep1-new search criteria Keck JM, et al. (2011)
    View Run MLP2 #19a Asynchronous Prep1-new search criteria 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 SPT21 NRD1 1 Unpublished Fields Lab Data

    Microscopy / Localization Data

    New Feature: Upload Your Own Microscopy Data

      PROTEIN(S) PUBLICATION
    View Data NRD1 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..200] MSA 6.475994 View MSA. No confident structure predictions are available.
    2 View Details [201..301] PSI-BLAST 52.69897 Nuclear ribonucleoprotein A1 (RNP A1, UP1)
    3 View Details [302..413] PSI-BLAST 52.69897 Nuclear ribonucleoprotein A1 (RNP A1, UP1)
    4 View Details [414..508] PSI-BLAST 36.69897 Hu antigen D (Hud)
    5 View Details [509..575] deduced N/A No confident structure predictions are available.

    Functions predicted (by domain):

    # Gene Ontology predictions
    1 No functions predicted.
    2
    Term Confidence Notes
  • nucleic acid binding
    		•  4.50398990564944 bayes_pls_golite062009
  • binding
    		•  4.16717332578111 bayes_pls_golite062009
  • RNA binding
    		•  2.92438188845619 bayes_pls_golite062009
  • transcription regulator activity
    		•  2.18211199677674 bayes_pls_golite062009
  • mRNA binding
    		•  1.94495589345842 bayes_pls_golite062009
  • DNA binding
    		•  1.73925834998328 bayes_pls_golite062009
  • hydrolase activity, acting on ester bonds
    		•  1.59667241219553 bayes_pls_golite062009
  • protein binding
    		•  1.32954276279597 bayes_pls_golite062009
  • transcription factor activity
    		•  0.873765500321315 bayes_pls_golite062009
    		• 0.84116054461637 bayes_pls_golite062009
  • RNA polymerase II transcription factor activity
    		•  0.632534695085793 bayes_pls_golite062009
  • hydrolase activity
    		•  0.520121701073354 bayes_pls_golite062009
  • sequence-specific DNA binding
    		•  0.294937517750882 bayes_pls_golite062009
  • general RNA polymerase II transcription factor activity
    		•  0.100880394187931 bayes_pls_golite062009
    3
    Term Confidence Notes
  • nucleic acid binding
    		•  4.50398990564944 bayes_pls_golite062009
  • binding
    		•  4.16717332578111 bayes_pls_golite062009
  • RNA binding
    		•  2.92438188845619 bayes_pls_golite062009
  • transcription regulator activity
    		•  2.18211199677674 bayes_pls_golite062009
  • mRNA binding
    		•  1.94495589345842 bayes_pls_golite062009
  • DNA binding
    		•  1.73925834998328 bayes_pls_golite062009
  • hydrolase activity, acting on ester bonds
    		•  1.59667241219553 bayes_pls_golite062009
  • protein binding
    		•  1.32954276279597 bayes_pls_golite062009
  • transcription factor activity
    		•  0.873765500321315 bayes_pls_golite062009
    		• 0.84116054461637 bayes_pls_golite062009
  • RNA polymerase II transcription factor activity
    		•  0.632534695085793 bayes_pls_golite062009
  • hydrolase activity
    		•  0.520121701073354 bayes_pls_golite062009
  • sequence-specific DNA binding
    		•  0.294937517750882 bayes_pls_golite062009
  • general RNA polymerase II transcription factor activity
    		•  0.100880394187931 bayes_pls_golite062009
    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: 0.99

    Source: Reynolds et al. (2008)

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