RRP40 exosome non-catalytic core subunit RRP40 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Gene symbol: RRP40
Gene description: exosome non-catalytic core subunit RRP40
Primary source: FungiDB:YOL142W
Locus tag: YOL142W
See related: SGD:S000005502; AllianceGenome:SGD:S000005502; VEuPathDB:YOL142W
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Also known as: MTR14
Summary: Enables RNA binding activity and manganese ion binding activity. Involved in exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA); nuclear polyadenylation-dependent rRNA catabolic process; and nuclear polyadenylation-dependent tRNA catabolic process. Part of cytoplasmic exosome (RNase complex) and nuclear exosome (RNase complex). Used to study pontocerebellar hypoplasia type 1B. Human ortholog(s) of this gene implicated in pontocerebellar hypoplasia type 1B. Orthologous to human EXOSC3 (exosome component 3). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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See RRP40 in Genome Data Viewer

Location:: chromosome: XV

Exon count:: 1

Sequence:: Chromosome: XV; NC_001147.6 (55558..56280)

Chromosome XV - NC_001147.6 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001147.6

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Mutations of EXOSC3/Rrp40p associated with pontocerebellar hypoplasia with progressive cerebral atrophy impact ribosomal RNA processing functions of the exosome in S. cerevisiae.
Title: Mutations of EXOSC3/Rrp40p associated with neurological diseases impact ribosomal RNA processing functions of the exosome in S. cerevisiae.
The three cap proteins (Csl4, Rrp4 and Rrp40) and the nuclease (Rrp44) are multidomain proteins with the expected conformational variability.
Title: Structure determination of an 11-subunit exosome in complex with RNA by molecular replacement.
We present the crystal structure of the Rrp40 exosome subunit from Saccharomyces cerevisiae at a resolution of 2.2 A.
Title: Structural and biochemical characterization of the yeast exosome component Rrp40.

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Pathways from PubChem

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Homology

Orthologs from OrthoDB

Gene Ontology Provided by SGD

Function	Evidence Code	Pubs
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables manganese ion binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in CUT catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in TRAMP-dependent tRNA surveillance pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in TRAMP-dependent tRNA surveillance pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in U4 snRNA 3'-end processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	IBA Inferred from Biological aspect of Ancestor more info
involved_in exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear polyadenylation-dependent rRNA catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in nuclear polyadenylation-dependent rRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	IBA Inferred from Biological aspect of Ancestor more info
involved_in poly(A)-dependent snoRNA 3'-end processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in rRNA processing	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
part_of cytoplasmic exosome (RNase complex)	IBA Inferred from Biological aspect of Ancestor more info
part_of cytoplasmic exosome (RNase complex)	IDA Inferred from Direct Assay more info	PubMed
part_of exosome (RNase complex)	IEA Inferred from Electronic Annotation more info
part_of nuclear exosome (RNase complex)	IBA Inferred from Biological aspect of Ancestor more info
part_of nuclear exosome (RNase complex)	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: exosome non-catalytic core subunit RRP40

NP_014499.2

Exosome non-catalytic core component; involved in 3'-5' RNA processing and degradation in both the nucleus and the cytoplasm; predicted to contain both S1 and KH RNA binding domains; mutations in the human homolog, EXOSC3, cause pontocerebellar hypoplasia with motor neuron degeneration

NCBI Reference Sequences (RefSeq)

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Genome Annotation

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference assembly

Genomic

NC_001147.6 Reference assembly

Range

55558..56280

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001183396.2 → NP_014499.2 TPA: exosome non-catalytic core subunit RRP40 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_014499.2

Status: REVIEWED

UniProtKB/Swiss-Prot

D6W1S7, E9P8Z4, Q08285

UniProtKB/TrEMBL

A0A6A5Q6Y9, A6ZN70, B3LIS5, B5VRB9, C7GV17, C8ZHH5, G2WM96, N1P307

Conserved Domains (1) summary

COG1097
Location:1 → 240

Rrp4; Exosome complex RNA-binding protein Rrp4, contains S1 and KH domains [Translation, ribosomal structure and biogenesis]