PRP28 mRNA splicing protein PRP28 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: PRP28
Official Full Name: mRNA splicing protein PRP28
Primary source: SGD:S000002651
Locus tag: YDR243C
See related: AllianceGenome:SGD:S000002651; FungiDB:YDR243C; VEuPathDB:YDR243C
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 RNA binding activity and first spliceosomal transesterification activity. Involved in mRNA 5'-splice site recognition. Part of U5 snRNP. Orthologous to human DDX23 (DEAD-box helicase 23). [provided by Alliance of Genome Resources, Nov 2024]
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Genomic context

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See PRP28 in Genome Data Viewer

Location:: chromosome: IV

Exon count:: 1

Sequence:: Chromosome: IV; NC_001136.10 (948518..950284, complement)

Chromosome IV - NC_001136.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001136.10

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Activation of Prp28 ATPase by phosphorylated Npl3 at a critical step of spliceosome remodeling.
Title: Activation of Prp28 ATPase by phosphorylated Npl3 at a critical step of spliceosome remodeling.
Cellular fitness can be restored by compensatory mutations that alter either the splicing machinery per se or the Spt-Ada-Gcn5 acetyltransferase transcription co-activator complex in the cells with no Prp28. Biochemical and genetic analysis revealed that slowing down transcription compensates for splicing deficiency, which in turn boosts cellular fitness.
Title: Adaptive transcription-splicing resynchronization upon losing an essential splicing factor.
The study demonstrated that yeast Prp28 is a bona fide RNA-dependent ATPase.
Title: Crystal structure, mutational analysis and RNA-dependent ATPase activity of the yeast DEAD-box pre-mRNA splicing factor Prp28.
The Prp8 suppressor partially corrected both the early assembly and later activation defects of prp28-1, supporting a role for this U5 snRNP protein in both the ATP-independent and ATP-dependent functions of Prp28.
Title: An unanticipated early function of DEAD-box ATPase Prp28 during commitment to splicing is modulated by U5 snRNP protein Prp8.
The subdomain linker in Prp28p plays important roles both in splicing efficiency and in proofreading of 5' splice site.
Title: Splicing proofreading at 5' splice sites by ATPase Prp28p.

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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 RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA helicase activity	IEA Inferred from Electronic Annotation more info
enables RNA helicase activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables first spliceosomal transesterification activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables helicase activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in RNA processing	IEA Inferred from Electronic Annotation more info
involved_in RNA splicing	IEA Inferred from Electronic Annotation more info
involved_in mRNA 5'-splice site recognition	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in ribonucleoprotein complex biogenesis	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of U5 snRNP	IDA Inferred from Direct Assay more info	PubMed
part_of catalytic step 2 spliceosome	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	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: mRNA splicing protein PRP28

NP_010529.3

EC 3.6.4.13

Pre-mRNA splicing factor; RNA binding protein involved in RNA isomerization at the 5' splice site and for exchange of U6 for U1 snRNA at the 5' splice site; similar to the RNA helicases of the DEAD-box family

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_001136.10 Reference assembly

Range

948518..950284 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001180551.3 → NP_010529.3 TPA: mRNA splicing protein PRP28 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_010529.3

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VSM3, P20450, P23394

UniProtKB/TrEMBL

B3LG46, B5VGC9, N1P522

Conserved Domains (1) summary

COG0513
Location:143 → 580

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