PRP43 DEAH-box ATP-dependent RNA helicase PRP43 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: PRP43
Official Full Name: DEAH-box ATP-dependent RNA helicase PRP43
Primary source: SGD:S000003088
Locus tag: YGL120C
See related: AllianceGenome:SGD:S000003088; FungiDB:YGL120C; VEuPathDB:YGL120C
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 helicase activity. Involved in RNA processing. Located in mitochondrion. Part of post-mRNA release spliceosomal complex. Orthologous to several human genes including DHX15 (DEAH-box helicase 15). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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See PRP43 in Genome Data Viewer

Location:: chromosome: VII

Exon count:: 1

Sequence:: Chromosome: VII; NC_001139.9 (281634..283937, complement)

Chromosome VII - NC_001139.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001139.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The G-patch activators Pfa1 and PINX1 exhibit different modes of interaction with the Prp43 RNA helicase.
Title: The G-patch activators Pfa1 and PINX1 exhibit different modes of interaction with the Prp43 RNA helicase.
These data indicate that the U2 snRNP-intron interaction is Prp43's major target.
Title: The target of the DEAH-box NTP triphosphatase Prp43 in Saccharomyces cerevisiae spliceosomes is the U2 snRNP-intron interaction.
Using Prp43 F357A mutants or pyrimidine nucleotides, we show that the lack of stacking of the nucleotide base to the F-motif decouples the NTPase and helicase activities of Prp43. In contrast the R159A mutant (R-motif) showed reduced ATPase and helicase activities.
Title: Functional link between DEAH/RHA helicase Prp43 activation and ATP base binding.
Study shows the crystal structure of Prp43p bound to single-stranded poly-uracil RNA and reveals differences with viral ATPases in the RecA1 domain but with striking similarities with viral ATPases in the RecA2 domain of the catalytic core, including both a prominent beta-hairpin that bookends the 5' end of the RNA stack and a dynamic motif Va that is implicated in mediating translocation.
Title: Structure of the DEAH/RHA ATPase Prp43p bound to RNA implicates a pair of hairpins and motif Va in translocation along RNA.
Ntr1 and Ntr2 may act as 'doorkeepers' and both cofactors may inspect the RNP structure of spliceosomal complexes thereby targeting suboptimal spliceosomes for Prp43-mediated disassembly.
Title: Regulation of Prp43-mediated disassembly of spliceosomes by its cofactors Ntr1 and Ntr2.
Results show that Prp43 expression is regulated by Cmg1 which stimulates its RNA helicase activity.
Title: Protein cofactor competition regulates the action of a multifunctional RNA helicase in different pathways.
Prp43 differentially interacts with g-patch domains in Spp382, Sqs1, and Pxr1 G.
Title: Limited portability of G-patch domains in regulators of the Prp43 RNA helicase required for pre-mRNA splicing and ribosomal RNA maturation in Saccharomyces cerevisiae.
This study investigated the activation of Prp43 by Ntr1 in the presence and absence of RNA substrate.
Title: Insights into the activation of the helicase Prp43 by biochemical studies and structural mass spectrometry.
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.
Prp43p promotes the discard of suboptimal and optimal 5' exon and lariat intermediates indiscriminately.
Title: Spliceosome discards intermediates via the DEAH box ATPase Prp43p.

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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 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	IDA Inferred from Direct Assay more info	PubMed
enables RNA helicase activity	IEA Inferred from Electronic Annotation more info
enables RNA helicase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables helicase activity	IBA Inferred from Biological aspect of Ancestor 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 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 processing	IEA Inferred from Electronic Annotation more info
involved_in maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in maturation of SSU-rRNA	IGI Inferred from Genetic Interaction more info	PubMed
involved_in maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in rRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ribonucleoprotein complex biogenesis	IEA Inferred from Electronic Annotation more info
involved_in ribosomal large subunit biogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in spliceosomal complex disassembly	IDA Inferred from Direct Assay more info	PubMed
involved_in spliceosomal complex disassembly	IGI Inferred from Genetic Interaction more info	PubMed

Component	Evidence Code	Pubs
part_of 90S preribosome	HDA more info	PubMed
located_in mitochondrion	HDA more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info
part_of post-mRNA release spliceosomal complex	IMP Inferred from Mutant Phenotype more info	PubMed
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 ATP-dependent RNA helicase PRP43

NP_011395.1

EC 3.6.4.13

RNA helicase in the DEAH-box family; functions in both RNA polymerase I and polymerase II transcript metabolism; catalyzes removal of U2, U5, and U6 snRNPs from the postsplicing lariat-intron ribonucleoprotein complex; required for efficient biogenesis of both small- and large-subunit rRNAs; acts with Sqs1p to promote 20S to 18S rRNA processing catalyzed by endonuclease Nob1p

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_001139.9 Reference assembly

Range

281634..283937 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001180985.1 → NP_011395.1 TPA: DEAH-box ATP-dependent RNA helicase PRP43 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_011395.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VU28, P53131

UniProtKB/TrEMBL

A6ZU62, B3LHI0, C7GM13, G2WDY2, N1P5D0

Conserved Domains (1) summary

COG1643
Location:55 → 753

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