CDC39 CCR4-NOT core subunit CDC39 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: CDC39
Official Full Name: CCR4-NOT core subunit CDC39
Primary source: SGD:S000000689
Locus tag: YCR093W
See related: AllianceGenome:SGD:S000000689; FungiDB:YCR093W; VEuPathDB:YCR093W
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: NOT1; ROS1; SMD6
Summary: Enables ATPase activator activity. Involved in several processes, including negative regulation of cytoplasmic mRNA processing body assembly; positive regulation of RNA metabolic process; and pseudohyphal growth. Located in cytoplasm and nucleus. Part of CCR4-NOT core complex. Human ortholog(s) of this gene implicated in Vissers-Bodmer syndrome and holoprosencephaly 12. Orthologous to human CNOT1 (CCR4-NOT transcription complex subunit 1). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See CDC39 in Genome Data Viewer

Location:: chromosome: III

Exon count:: 1

Sequence:: Chromosome: III; NC_001135.5 (280117..286443)

Chromosome III - NC_001135.5 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001135.5

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events.
Title: Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events.
The Ccr4-Not complex regulates TORC1 signaling and mitochondrial metabolism by promoting vacuole V-ATPase activity.
Title: The Ccr4-Not complex regulates TORC1 signaling and mitochondrial metabolism by promoting vacuole V-ATPase activity.
Studies indicate that the Ccr4 (carbon catabolite repressed 4)-Not (negative on TATA-less) complex has been connected to every step of the mRNA lifecycle.
Title: Ccr4-Not is at the core of the eukaryotic gene expression circuitry.
The interplay between Ccr4-Not and Rpb4/7 described here suggests a mechanism for how the cell coordinates mRNA synthesis and decay
Title: The Rpb4/7 module of RNA polymerase II is required for carbon catabolite repressor protein 4-negative on TATA (Ccr4-not) complex to promote elongation.
Not2 and Not5 have extended regions that wrap around Not1 and around their globular domains, the Not boxes.
Title: Structure and RNA-binding properties of the Not1-Not2-Not5 module of the yeast Ccr4-Not complex.
A 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.
Results describe the structure of the purified CCR4-NOT complex as determined by electron microscopy.
Title: Insights into the structure of the CCR4-NOT complex by electron microscopy.
the Ccr4-Not complex independently controls TFIID promoter distribution and Msn2-dependent trans-activation through a process involving a Glc7/Bud14 phosphatase
Title: The Ccr4-Not complex independently controls both Msn2-dependent transcriptional activation--via a newly identified Glc7/Bud14 type I protein phosphatase module--and TFIID promoter distribution.

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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 ATPase activator activity	IDA Inferred from Direct Assay more info	PubMed
enables molecular adaptor activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in negative regulation of cytoplasmic mRNA processing body assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of cytoplasmic mRNA processing body assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of translation	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 catabolic process, deadenylation-dependent decay	IDA Inferred from Direct Assay more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear-transcribed mRNA poly(A) tail shortening	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription elongation by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in pseudohyphal growth	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cell cycle	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IPI Inferred from Physical Interaction more info	PubMed
involved_in response to pheromone triggering conjugation with cellular fusion	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transcription elongation by RNA polymerase II	IGI Inferred from Genetic Interaction 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 core complex	IBA Inferred from Biological aspect of Ancestor more info
part_of CCR4-NOT core complex	IEA Inferred from Electronic Annotation more info
part_of CCR4-NOT core complex	IPI Inferred from Physical Interaction more info	PubMed
is_active_in P-body	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleus	IDA Inferred from Direct Assay 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 subunit CDC39

NP_010017.2

Subunit of the CCR4-NOT1 core complex; this complex has multiple roles in the regulation of mRNA levels including regulation of transcription and destabilization of mRNA by deadenylation; basal transcription factor that increases initiation and elongation; activates the ATPase activity of Dhh1p, resulting in processing body disassembly

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_001135.5 Reference assembly

Range

280117..286443

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001178799.1 → NP_010017.2 TPA: CCR4-NOT core subunit CDC39 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_010017.2

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VR93, P25655

UniProtKB/TrEMBL

A6ZTR4

Conserved Domains (1) summary

COG5103
Location:1 → 2108

CDC39; Cell division control protein, negative regulator of transcription [Cell division and chromosome partitioning / Transcription]