NAM7 ATP-dependent RNA helicase NAM7 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Gene symbol: NAM7
Gene description: ATP-dependent RNA helicase NAM7
Primary source: FungiDB:YMR080C
Locus tag: YMR080C
See related: SGD:S000004685; AllianceGenome:SGD:S000004685; VEuPathDB:YMR080C
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: IFS2; MOF4; SUP113; SUT2; UPF1
Summary: Enables ATP hydrolysis activity; RNA helicase activity; and ribosomal small subunit binding activity. Involved in several processes, including intracellular mRNA localization; protein ubiquitination; and regulation of gene expression. Located in cytoplasm. Part of polysome. Orthologous to human UPF1 (UPF1 RNA helicase and ATPase). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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See NAM7 in Genome Data Viewer

Location:: chromosome: XIII

Exon count:: 1

Sequence:: Chromosome: XIII; NC_001145.3 (426712..429627, complement)

Chromosome XIII - NC_001145.3 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001145.3

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Nuclear SR-protein mediated mRNA quality control is continued in cytoplasmic nonsense-mediated decay.
Title: Nuclear SR-protein mediated mRNA quality control is continued in cytoplasmic nonsense-mediated decay.
Inhibition of post-termination ribosome recycling at premature termination codons in UPF1 ATPase mutants.
Title: Inhibition of post-termination ribosome recycling at premature termination codons in UPF1 ATPase mutants.
The expression of Rpb10, a small subunit common to RNA polymerases, is modulated by the R3H domain-containing Rbs1 protein and the Upf1 helicase.
Title: The expression of Rpb10, a small subunit common to RNA polymerases, is modulated by the R3H domain-containing Rbs1 protein and the Upf1 helicase.
Nonsense-mediated mRNA decay involves two distinct Upf1-bound complexes.
Title: Nonsense-mediated mRNA decay involves two distinct Upf1-bound complexes.
Identification of the 1C domain of Upf1, an alpha-helical insertion in the RecA helicase core, to be essential for ribosome binding. The L1 stalk of 25S rRNA is the binding site for Upf1 on the ribosome.
Title: Directed hydroxyl radical probing reveals Upf1 binding to the 80S ribosomal E site rRNA at the L1 stalk.
UPF1, a highly processive helicase central to nonsense-mediated mRNA decay (NMD), tightly holds onto NA, allowing long lasting action. UPF1 mutants with variable grip on DNA show that grip tightness dictates helicase residence time and processivity.
Title: UPF1-like helicase grip on nucleic acids dictates processivity.
The propose that the Sse1/Hsp70 complex maintains the solubility of FLAG-Pgk1-300, thereby stimulating its Upf-dependent degradation by the proteasomes.
Title: Crucial role of ATP-bound Sse1 in Upf1-dependent degradation of the truncated product.
The study provides evidence that two tyrosines within a phospho-motif of Upf1 act redundantly to promote ATP hydrolysis, Nonsense-Mediated mRNA Decay efficiency and translation termination fidelity.
Title: Identification and functional analysis of novel phosphorylation sites in the RNA surveillance protein Upf1.
The cysteine- and histidine-rich (CH) domain and the RNA helicase domain of yeast Upf1 can engage in two new types of molecular interactions: an intramolecular interaction between these two domains and self-association of each of these domains.
Title: Intra- and intermolecular regulatory interactions in Upf1, the RNA helicase central to nonsense-mediated mRNA decay in yeast.
The upf1Delta mutant contained elevated copper levels in the vacuole relative to wild-type yeast cells, after both strains were exposed to elevated copper levels. Copper tolerance by the upf1Delta mutant is dependent on the presence of CTR2.
Title: Physiological basis of copper tolerance of Saccharomyces cerevisiae nonsense-mediated mRNA decay mutants.

Submit: New GeneRIF Correction See all GeneRIFs (16)

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 ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IDA Inferred from Direct Assay more info	PubMed
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA helicase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA helicase activity	IDA Inferred from Direct Assay more info	PubMed
enables RNA helicase activity	IEA Inferred from Electronic Annotation more info
enables helicase activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables mRNA binding	HDA more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables ribosomal small subunit binding	IDA Inferred from Direct Assay more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info
enables zinc ion binding	RCA inferred from Reviewed Computational Analysis more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA recombination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in intracellular mRNA localization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay	IGI Inferred from Genetic Interaction more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IBA Inferred from Biological aspect of Ancestor more info
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IEA Inferred from Electronic Annotation more info
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in protein ubiquitination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein ubiquitination	IPI Inferred from Physical Interaction more info	PubMed
involved_in regulation of translational termination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in silent mating-type cassette heterochromatin formation	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	HDA more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: ATP-dependent RNA helicase NAM7

NP_013797.1

EC 3.6.4.12

EC 3.6.4.13

ATP-dependent RNA helicase of the SFI superfamily; involved in nonsense mediated mRNA decay; required for efficient translation termination at nonsense codons and targeting of NMD substrates to P-bodies; binds to the small ribosomal subunit via an interaction with Rps26; forms cytoplasmic foci upon DNA replication stress

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_001145.3 Reference assembly

Range

426712..429627 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001182579.1 → NP_013797.1 TPA: ATP-dependent RNA helicase NAM7 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_013797.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VZQ4, P30771

UniProtKB/TrEMBL

B3LLX3, B5VPK6, C7GL44, C8ZET3, N1P5H0

Conserved Domains (1) summary

COG1112
Location:84 → 851

DNA2; Superfamily I DNA and/or RNA helicase [Replication, recombination and repair]