Protein Overview: RRP42

General Information:
Name(s) found:	RRP42 / YDL111C [SGD]
Description(s) found: Found 26 descriptions. SHOW ALL	Exosome non-catalytic core component; involved in 3'-5' RNA processing and degradation in both the nucleus and the cytoplasm; has similarity to E. coli RNase PH and to human hRrp42p (EXOSC7) [SGD]
Organism:	Saccharomyces cerevisiae
Length:	265 amino acids
Gene Ontology:
Cellular Component:	cytoplasmic exosome (RNase complex) [IDA] nuclear exosome (RNase complex) [IDA] nuclear outer membrane [TAS]
Biological Process:	mRNA catabolic process [IPI]
Molecular Function:	3'-5'-exoribonuclease activity [TAS]

Sequence:

Sequence:
[PDR BLAST]
[ProtParam]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSLSVAEKSY LYDSLASTPS IRPDGRLPHQ FRPIEIFTDF LPSSNGSSRI IASDGSECIV  60
   61 SIKSKVVDHH VENELLQVDV DIAGQRDDAL VVETITSLLN KVLKSGSGVD SSKLQLTKKY 120
  121 SFKIFVDVLV ISSHSHPVSL ISFAIYSALN STYLPKLISA FDDLEVEELP TFHDYDMVKL 180
  181 DINPPLVFIL AVVGNNMLLD PAANESEVAN NGLIISWSNG KITSPIRSVA LNDSNVKSFK 240
  241 PHLLKQGLAM VEKYAPDVVR SLENL

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 (2010) (Unpublished Data)		CSL4 DIS3 LRP1 MPP6 MTR3 RRP4 RRP40 RRP42 RRP43 RRP45 RRP46 RRP6 SKI6 SKI7 SRP1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 LRP1 MAM33 MLC1 MTR3 MYO2 NMD5 RRP4 RRP40 RRP42 RRP43 RRP45 RRP46 RRP6 SAM1 SHE4 SKI2 SKI3 SKI6 SKI7 SRP1 UTP10 UTP20 UTP22 YIR035C
View Details	Ho Y, et al. (2002)		APA1 GAR1 LSM2 LSM8 QCR2 RPN12 RPN8 RRP42 SMB1 TIF6 YGL117W
View Details	Qiu et al. (2008)		CSL4 DIS3 MTR3 RRP4 RRP40 RRP42 RRP43 RRP45 RRP46 RRP6 SKI6

Mass Spectrometry Data

No mass spectrometry results found for this protein.

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View Screen	YJR056C	RRP42	1	Unpublished Fields Lab Data
View Screen	NUP2	RRP42	1	Unpublished Fields Lab Data

Microscopy / Localization Data

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	PROTEIN(S)	PUBLICATION
View Data	RRP42	Huh WK, et al. (2003)
View Data	RRP42 and NOP56	Huh WK, et al. (2003)

Protein Structure Data

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[View Top Sequence Alignments] [Show Ginzu Version Information]

Domains predicted:

#		Region(s)	Method	Confidence	Match Description
1	View Details	[1..32] [163..249]	PSI-BLAST	47.69897	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	[33..162] [250..265]	PSI-BLAST	47.69897	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

Functions predicted (by domain):

Gene Ontology predictions

Term	Confidence	Notes
exoribonuclease activity	7.55877202113513	bayes_pls_golite062009
ribonuclease activity	7.54644729272203	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	7.5310318714913	bayes_pls_golite062009
3'-5'-exoribonuclease activity	6.46930372693262	bayes_pls_golite062009
3'-5' exonuclease activity	4.29895100594643	bayes_pls_golite062009
exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	3.83939403332553	bayes_pls_golite062009
exonuclease activity	3.40686901061667	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	2.86434572018929	bayes_pls_golite062009
RNA binding	2.05527376734941	bayes_pls_golite062009
hydrolase activity	1.55476709794855	bayes_pls_golite062009
structural constituent of ribosome	1.2826764117718	bayes_pls_golite062009
transcription regulator activity	1.20748032530392	bayes_pls_golite062009
mRNA binding	1.17402119891853	bayes_pls_golite062009
nucleic acid binding	1.05662964529454	bayes_pls_golite062009
structural molecule activity	0.9404621246304	bayes_pls_golite062009
binding	0.907487229190259	bayes_pls_golite062009
catalytic activity	0.878454819018611	bayes_pls_golite062009
DNA binding	0.828609700556836	bayes_pls_golite062009
nuclease activity	0.69721312877891	bayes_pls_golite062009

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:	0.88

Source: Reynolds et al. (2008)

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2