SKI2 SKI complex RNA helicase subunit SKI2 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: SKI2
Official Full Name: SKI complex RNA helicase subunit SKI2
Primary source: SGD:S000004390
Locus tag: YLR398C
See related: AllianceGenome:SGD:S000004390; FungiDB:YLR398C; VEuPathDB:YLR398C
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Saccharomyces cerevisiae S288C (strain: S288C)
Lineage: Eukaryota; Fungi; Dikarya; Ascomycota; Saccharomycotina; Saccharomycetes; Saccharomycetales; Saccharomycetaceae; Saccharomyces
Summary: Enables mRNA binding activity. Involved in nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay and nuclear-transcribed mRNA catabolic process, non-stop decay. Located in cytoplasm. Part of Ski complex. Used to study trichohepatoenteric syndrome 2. Human ortholog(s) of this gene implicated in trichohepatoenteric syndrome 2. Orthologous to human SKIC2 (SKI2 subunit of superkiller complex). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See SKI2 in Genome Data Viewer

Location:: chromosome: XII

Exon count:: 1

Sequence:: Chromosome: XII; NC_001144.5 (915156..919019, complement)

Chromosome XII - NC_001144.5 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001144.5

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Ski2, Ski3, and Ski8 assemble in a tetramer with 1:1:2 stoichiometry; 370 kDa core complex shows that Ski3 forms an array of 33 tetratricopeptide repeat motifs organized in N-terminal and C-terminal arms. The C-terminal arm of Ski3 and the two Ski8 subunits position the helicase core of Ski2 centrally within the complex, enhancing RNA binding.
Title: The yeast ski complex: crystal structure and RNA channeling to the exosome complex.
the 2.4 A resolution crystal structure of the 113 kDa helicase region of Saccharomyces cerevisiae Ski2 was determined.
Title: The crystal structure of S. cerevisiae Ski2, a DExH helicase associated with the cytoplasmic functions of the exosome.
Inactivating the Ski complex by mutating conserved residues in the DEVH helicase motif of Ski2 did not abrogate its interaction with Ski7p, indicating that Ski2p function is not necessary for this interaction.
Title: Domain interactions within the Ski2/3/8 complex and between the Ski complex and Ski7p.

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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 ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H2AZ histone chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H3-H4 histone complex chaperone activity	IEA Inferred from Electronic Annotation more info
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA clamp loader activity	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation more info
enables chromatin extrusion motor activity	IEA Inferred from Electronic Annotation more info
enables cohesin loader 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

Process	Evidence Code	Pubs
involved_in RNA catabolic process	IEA Inferred from Electronic Annotation more info
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in defense response to virus	IEA Inferred from Electronic Annotation more info
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	IBA Inferred from Biological aspect of Ancestor more info
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, non-stop decay	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of translation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of Ski complex	IBA Inferred from Biological aspect of Ancestor more info
part_of Ski complex	IDA Inferred from Direct Assay more info	PubMed
part_of Ski complex	IPI Inferred from Physical Interaction more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: SKI complex RNA helicase subunit SKI2

NP_013502.3

EC 3.6.4.13

Ski complex component and putative RNA helicase; mediates 3'-5' RNA degradation by the cytoplasmic exosome; null mutants have superkiller phenotype of increased viral dsRNAs and are synthetic lethal with mutations in 5'-3' mRNA decay; mutations in the human ortholog, SKIV2L, causes Syndromic diarrhea/Trichohepatoenteric (SD/THE) syndrome

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_001144.5 Reference assembly

Range

915156..919019 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001182286.3 → NP_013502.3 TPA: SKI complex RNA helicase subunit SKI2 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_013502.3

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VZ33, P35207, Q06047

UniProtKB/TrEMBL

B3RHR3, N1NYS9

Conserved Domains (1) summary

COG4581
Location:137 → 1287

Dob10; Superfamily II RNA helicase [Replication, recombination and repair]