PRP16 DEAH-box RNA helicase PRP16 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: PRP16
Official Full Name: DEAH-box RNA helicase PRP16
Primary source: SGD:S000001794
Locus tag: YKR086W
See related: AllianceGenome:SGD:S000001794; FungiDB:YKR086W; VEuPathDB:YKR086W
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: PRP23; RNA16
Summary: Enables ATP-dependent activity, acting on RNA. Contributes to second spliceosomal transesterification activity. Involved in RNA exon ligation; generation of catalytic spliceosome for second transesterification step; and snRNA modification. Part of U2-type catalytic step 2 spliceosome. Used to study retinitis pigmentosa. Human ortholog(s) of this gene implicated in retinitis pigmentosa 84. Orthologous to human DHX38 (DEAH-box helicase 38). [provided by Alliance of Genome Resources, Nov 2024]
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Genomic context

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See PRP16 in Genome Data Viewer

Location:: chromosome: XI

Exon count:: 1

Sequence:: Chromosome: XI; NC_001143.9 (599857..603072)

Chromosome XI - NC_001143.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001143.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

An ATP-independent role for Prp16 in promoting aberrant splicing.
Title: An ATP-independent role for Prp16 in promoting aberrant splicing.
In the process of pre-mRNA splicing, Cwc25 binds tightly to the spliceosome after the reaction and is then removed from the spliceosome, which normally requires Prp16 and ATP hydrolysis, to allow the occurrence of the second reaction.
Title: A central role of Cwc25 in spliceosome dynamics during the catalytic phase of pre-mRNA splicing.
At the catalytic stage of splicing, suboptimal splice sites are repressed by the DEAH-box ATPases Prp16 and Prp22. study shows that these ATPases function further by enabling the spliceosome to search for and utilize alternative branch sites and 3' splice sites.
Title: Spliceosomal DEAH-Box ATPases Remodel Pre-mRNA to Activate Alternative Splice Sites.
Results indicate that the prp16-302 mutation in Prp16 stabilizes Cwc2 interactions with U6 snRNA and destabilizes Cwc2 interactions with pre-mRNA, indicating antagonistic functions of Cwc2 and Prp16.
Title: Remodeling of U2-U6 snRNA helix I during pre-mRNA splicing by Prp16 and the NineTeen Complex protein Cwc2.
In the absence of the C domain, Yju2-N domain is not stably associated with the spliceosome after lariat formation, and thus bypasses the need for Prp16.
Title: A weak spliceosome-binding domain of Yju2 functions in the first step and bypasses Prp16 in the second step of splicing.
NTR complex catalyzes the disassembly of affinity-purified spliceosomes arrested specifically after the ATP-dependent action of DEAH-box Prp2, Prp16, or Prp22 but not at steps before the action of these ATPases or upon their binding to the spliceosome.
Title: Link of NTR-mediated spliceosome disassembly with DEAH-box ATPases Prp2, Prp16, and Prp22.
The DEAH box ATPases Prp16 and Prp43 cooperate to proofread 5' splice site cleavage during pre-mRNA splicing.
Title: The DEAH box ATPases Prp16 and Prp43 cooperate to proofread 5' splice site cleavage during pre-mRNA splicing.
Prp16 remodels an interaction involving Isy1 in the transition between two steps of splicing
Title: The Isy1p component of the NineTeen complex interacts with the ATPase Prp16p to regulate the fidelity of pre-mRNA splicing.

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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 helicase activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent activity, acting on RNA	IDA Inferred from Direct Assay more info	PubMed
enables ATP-dependent activity, acting on RNA	IEA Inferred from Electronic Annotation more info
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
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 nucleic acid binding	IEA Inferred from Electronic Annotation more info
contributes_to second spliceosomal transesterification activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA exon ligation	IDA Inferred from Direct Assay more info	PubMed
involved_in RNA processing	IEA Inferred from Electronic Annotation more info
involved_in RNA splicing	IEA Inferred from Electronic Annotation more info
involved_in generation of catalytic spliceosome for second transesterification step	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
involved_in snRNA metabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in snRNA modification	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of U2-type catalytic step 2 spliceosome	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of ribonucleoprotein complex	IEA Inferred from Electronic Annotation more info
part_of spliceosomal complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: DEAH-box RNA helicase PRP16

NP_013012.3

EC 3.6.4.13

DEAH-box RNA helicase; involved in the second catalytic step of splicing and in exon ligation; exhibits ATP-dependent RNA unwinding activity; mediates the release of Yju2p and Cwc25p in the second step; in the absence of ATP, stabilizes the binding of Cwc25p to the spliceosome in the first catalytic step; missense mutation in human ortholog DHX38 associated with early-onset retinitis pigmentosa

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_001143.9 Reference assembly

Range

599857..603072

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001179876.3 → NP_013012.3 TPA: DEAH-box RNA helicase PRP16 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_013012.3

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VXE6, P15938

UniProtKB/TrEMBL

A7A045, B3LRG0, C7GXC4

Conserved Domains (1) summary

COG1643
Location:319 → 1071

HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]