POP2 CCR4-NOT core DEDD family RNase subunit POP2 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Gene symbol: POP2
Gene description: CCR4-NOT core DEDD family RNase subunit POP2
Primary source: FungiDB:YNR052C
Locus tag: YNR052C
See related: SGD:S000005335; AllianceGenome:SGD:S000005335; VEuPathDB:YNR052C
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: CAF1
Summary: Enables 3'-5'-exoribonuclease activity. Involved in nuclear-transcribed mRNA poly(A) tail shortening; positive regulation of transcription elongation from RNA polymerase II promoter; and transcription elongation from RNA polymerase II promoter. Located in P-body. Part of CCR4-NOT core complex. Orthologous to human CNOT7 (CCR4-NOT transcription complex subunit 7) and CNOT8 (CCR4-NOT transcription complex subunit 8). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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See POP2 in Genome Data Viewer

Location:: chromosome: XIV

Exon count:: 1

Sequence:: Chromosome: XIV; NC_001146.8 (719346..720647, complement)

Chromosome XIV - NC_001146.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001146.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Analyses of POL30 (PCNA) reveal positional effects in transient repression or bi-modal active/silent state at the sub-telomeres of S. cerevisiae.
Title: Analyses of POL30 (PCNA) reveal positional effects in transient repression or bi-modal active/silent state at the sub-telomeres of S. cerevisiae.
Yeast Puf3p-mediated mRNA decay is regulated by carbon source-specific differential interaction of Puf3p with Pop2p and Yak1p.
Title: Yeast Puf3p-mediated mRNA decay is regulated by carbon source-specific differential interaction of Puf3p with Pop2p and Yak1p.
Ccr4-Not complex subunits Ccr4, Caf1, and Not4 are novel proteolysis factors promoting the degradation of ubiquitin-dependent substrates by the 26S proteasome.
Title: Ccr4-Not complex subunits Ccr4, Caf1, and Not4 are novel proteolysis factors promoting the degradation of ubiquitin-dependent substrates by the 26S proteasome.
Alternative RNA degradation pathways by the exonuclease Pop2p from Saccharomyces cerevisiae.
Title: Alternative RNA degradation pathways by the exonuclease Pop2p from Saccharomyces cerevisiae.
CAF-1 and Rtt101p function within the replication-coupled chromatin assembly network to promote H4 K16ac, preventing ectopic silencing.
Title: CAF-1 and Rtt101p function within the replication-coupled chromatin assembly network to promote H4 K16ac, preventing ectopic silencing.
Pan2 does not form canonical base-specific contacts. Instead, it recognizes the intrinsic stacked, helical conformation of poly(A) RNA. Using a fully reconstituted biochemical system, the study shows that disruption of this structure-for example, by incorporation of guanosine into poly(A)-inhibits deadenylation by both Pan2 and Caf1.
Title: The intrinsic structure of poly(A) RNA determines the specificity of Pan2 and Caf1 deadenylases.
Here, the authors report that yeast chromatin assembly factor 1 (CAF1), a conserved histone chaperone complex that deposits H3-H4 during DNA replication, binds a single H3-H4 heterodimer in solution.
Title: Insights into the molecular architecture and histone H3-H4 deposition mechanism of yeast Chromatin assembly factor 1.
The authors show that yeast chromatin assembly factor 1 binding to a histone H3-H4 dimer activates the Cac1 winged helix domain interaction with DNA. This drives the formation of a transient intermediate containing two chromatin assembly factor 1 complexes, each associated with one H3-H4 dimer. Here, the (H3-H4)2 tetramer is formed and deposited onto DNA.
Title: DNA-mediated association of two histone-bound complexes of yeast Chromatin Assembly Factor-1 (CAF-1) drives tetrasome assembly in the wake of DNA replication.
MIF4G domain positioned centrally within the Not1 protein recognizes Caf1, which in turn binds the LRR domain of Ccr4 and tethers the Ccr4 nuclease domain
Title: Architecture of the nuclease module of the yeast Ccr4-not complex: the Not1-Caf1-Ccr4 interaction.
tight connection between DNA synthesis and histone deposition during DNA replication mediated by H3K56ac/CAF1/Rtt106 provides a mechanism for the stabilization of advancing replication forks and the maintenance of genome integrity.
Title: Histone H3K56 acetylation, CAF1, and Rtt106 coordinate nucleosome assembly and stability of advancing replication forks.

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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 3'-5'-RNA exonuclease activity	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables exonuclease activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables poly(A)-specific ribonuclease activity	IBA Inferred from Biological aspect of Ancestor more info
enables poly(A)-specific ribonuclease activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in mRNA catabolic process	IEA Inferred from Electronic Annotation more info
involved_in nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	IBA Inferred from Biological aspect of Ancestor more info
involved_in nuclear-transcribed mRNA poly(A) tail shortening	IDA Inferred from Direct Assay more info	PubMed
involved_in nuclear-transcribed mRNA poly(A) tail shortening	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription elongation by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in transcription elongation by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of CCR4-NOT complex	IEA Inferred from Electronic Annotation more info
part_of CCR4-NOT core complex	IBA Inferred from Biological aspect of Ancestor more info
part_of CCR4-NOT core complex	IDA Inferred from Direct Assay more info	PubMed
is_active_in P-body	IBA Inferred from Biological aspect of Ancestor more info
located_in P-body	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in mating projection tip	HDA more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: CCR4-NOT core DEDD family RNase subunit POP2

NP_014450.3

EC 3.1.13.4

Subunit of Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation; exonuclease of the DEDD superfamily

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_001146.8 Reference assembly

Range

719346..720647 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001183229.3 → NP_014450.3 TPA: CCR4-NOT core DEDD family RNase subunit POP2 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_014450.3

Status: REVIEWED

UniProtKB/Swiss-Prot

D6W1M7, P39008

UniProtKB/TrEMBL

A0A8H4F9C4, B3LPJ1, C7GLK5, C8ZFT1, N1NWV3

Conserved Domains (1) summary

COG5228
Location:141 → 433

POP2; mRNA deadenylase subunit [RNA processing and modification]