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Protein Overview: RRP4

General Information:
Name(s) found: RRP4 / YHR069C [SGD]
Description(s) found:
Found 30 descriptions.
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  • Exosome non-catalytic core component; involved in 3'-5' RNA processing and degradation in both the nucleus and the cytoplasm; predicted to contain RNA binding domains; has similarity to human hRrp4p (EXOSC2) [SGD]
    • Organism: Saccharomyces cerevisiae
    Length: 359 amino acids

    Gene Ontology:
    Cellular Component: cytoplasmic exosome (RNase complex) [IDALink to PubMed article]
    nuclear exosome (RNase complex) [IDALink to PubMed article]
    nuclear outer membrane [TASLink to PubMed article]
    Biological Process: mRNA catabolic process [IMPLink to PubMed article]
    Molecular Function: 3'-5'-exoribonuclease activity [TASLink to PubMed article]
    RNA binding [ISSLink to PubMed article]


    Sequence:
    Sequence:
    [PDR BLAST]
    [ProtParam] 
          1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSEVITITKR NGAFQNSSNL SYNNTGISDD ENDEEDIYMH DVNSASKSES DSQIVTPGEL  60
   61 VTDDPIWMRG HGTYFLDNMT YSSVAGTVSR VNRLLSVIPL KGRYAPETGD HVVGRIAEVG 120
  121 NKRWKVDIGG KQHAVLMLGS VNLPGGILRR KSESDELQMR SFLKEGDLLN AEVQSLFQDG 180
  181 SASLHTRSLK YGKLRNGMFC QVPSSLIVRA KNHTHNLPGN ITVVLGVNGY IWLRKTSQMD 240
  241 LARDTPSANN SSSIKSTGPT GAVSLNPSIT RLEEESSWQI YSDENDPSIS NNIRQAICRY 300
  301 ANVIKALAFC EIGITQQRIV SAYEASMVYS NVGELIEKNV MESIGSDILT AEKMRGNGN

    Protein Complex Data

      PUBLICATION TOPOLOGY COCOMPLEXED PROTEINS
    View Details Riffle et al. (2010) (Unpublished Data) CSL4 DIS3 LRP1 MPP6 MTR3 RRP4 RRP40 RRP42 RRP43 RRP45 RRP46 RRP6 SKI6 SKI7 SRP1
    View Details (MIPS) Mewes HW, et al. (2004) DIS3 RRP4 RRP42 RRP43 RRP45 RRP46 SKI6
    View Details Krogan NJ, et al. (2006) CSL4 DDI1 DIS3 ENT3 LRP1 MPP6 MTR3 OSM1 RRP4 RRP40 RRP42 RRP43 RRP45 RRP46 RRP6 SKI6 SKI7 YBL055C
    View Details Gavin AC, et al. (2006) CSL4 DIS3 MTR3 RRP4 RRP40 RRP42 RRP43 RRP45 RRP46 RRP6 SKI6 SKI7
    View Details Gavin AC, et al. (2002) CMD1 CSL4 CTR9 DIS3 ECM16 GCN1 ISW1 LRP1 MAM33 MAS1 MAS2 MLC1 MTR3 MYO2 NMD5 RRP4 RRP40 RRP42 RRP43 RRP45 RRP46 RRP6 SAM1 SHE4 SKI2 SKI3 SKI6 SKI7 SMC4 SRP1 UTP10 UTP20 UTP22 YIR035C
    View Details Ho Y, et al. (2002) DIS3 EAF3 FIP1 HAS1 HPR1 KAP95 MES1 MFT1 NAM8 NOP6 NUP1 NUP2 NUP60 PAP1 PCT1 REB1 RNT1 RRP4 RRP43 RRP6 RTT103 SIF2 SIN3 SNU56 SRP1 STO1 THO2 TRA1 UME1 YPR090W
    View Details Qiu et al. (2008) CSL4 DIS3 MTR3 RRP4 RRP40 RRP42 RRP43 RRP45 RRP46 RRP6 SKI6

    Mass Spectrometry Data

    The following runs contain data for this protein:

      BAIT COMMENTS PUBLICATION
    View Run SPP382 No Comments Hazbun TR, et al. (2003)

    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

      PROTEIN(S) PUBLICATION
    View Data RRP4 Huh WK, et al. (2003)
    View Data RRP4 and NOP56 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..189] PSI-BLAST 23.69897 Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3; S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5
    2 View Details [190..287] MSA 2.200996 View MSA. No confident structure predictions are available.
    3 View Details [288..359] deduced N/A Confident ab initio structure predictions are available.

    Functions predicted (by domain):

    # Gene Ontology predictions
    1
    Term Confidence Notes
  • RNA binding
    		•  5.18414740305744 bayes_pls_golite062009
  • exoribonuclease activity
    		•  4.57899887224013 bayes_pls_golite062009
  • exoribonuclease activity, producing 5'-phosphomonoesters
    		•  4.54136587416505 bayes_pls_golite062009
  • ribonuclease activity
    		•  4.53127626527286 bayes_pls_golite062009
  • structural constituent of ribosome
    		•  3.89236528662255 bayes_pls_golite062009
  • mRNA binding
    		•  3.82977088614136 bayes_pls_golite062009
  • nucleic acid binding
    		•  3.68444148122352 bayes_pls_golite062009
  • structural molecule activity
    		•  3.54418030121155 bayes_pls_golite062009
  • 3'-5'-exoribonuclease activity
    		•  3.40736445988244 bayes_pls_golite062009
  • binding
    		•  2.8667878224392 bayes_pls_golite062009
    		• 1.63970610538963 bayes_pls_golite062009
  • hydrolase activity, acting on ester bonds
    		•  1.62417180482862 bayes_pls_golite062009
  • 3'-5' exonuclease activity
    		•  1.55351486913613 bayes_pls_golite062009
  • transcription regulator activity
    		•  1.43703138180882 bayes_pls_golite062009
  • exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters
    		•  1.42151567812515 bayes_pls_golite062009
  • aminoacyl-tRNA ligase activity
    		•  1.35850109411274 bayes_pls_golite062009
  • ligase activity, forming aminoacyl-tRNA and related compounds
    		•  1.35845277283398 bayes_pls_golite062009
  • ligase activity, forming carbon-oxygen bonds
    		•  1.35845277283398 bayes_pls_golite062009
  • exonuclease activity
    		•  1.25488463068335 bayes_pls_golite062009
  • DNA binding
    		•  1.20852534725468 bayes_pls_golite062009
  • exoribonuclease II activity
    		•  1.18248519339188 bayes_pls_golite062009
  • protein binding
    		•  0.934192915895039 bayes_pls_golite062009
  • hydrolase activity
    		•  0.704891843968224 bayes_pls_golite062009
  • mRNA 3'-UTR binding
    		•  0.489176583045793 bayes_pls_golite062009
  • transcription factor activity
    		•  0.386248501195543 bayes_pls_golite062009
  • ligase activity
    		•  0.346041081217685 bayes_pls_golite062009
  • structure-specific DNA binding
    		•  0.32222928997178 bayes_pls_golite062009
  • poly-pyrimidine tract binding
    		•  0.30467150200016 bayes_pls_golite062009
  • catalytic activity
    		•  0.161830442565647 bayes_pls_golite062009
  • aspartate-tRNA ligase activity
    		•  0.151650064901878 bayes_pls_golite062009
  • translation initiation factor activity
    		•  0.11625379846973 bayes_pls_golite062009
  • single-stranded DNA binding
    		•  0.1069917291606 bayes_pls_golite062009
  • DNA-directed RNA polymerase activity
    		•  0.0740938021136293 bayes_pls_golite062009
  • RNA polymerase activity
    		•  0.0740938021136293 bayes_pls_golite062009
    2 No functions predicted.
    3 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: 0.94

    Source: Reynolds et al. (2008)

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