DBP5 ATP-dependent RNA helicase DBP5 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: DBP5
Official Full Name: ATP-dependent RNA helicase DBP5
Primary source: SGD:S000005572
Locus tag: YOR046C
See related: AllianceGenome:SGD:S000005572; FungiDB:YOR046C; VEuPathDB:YOR046C
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: RAT8
Summary: Enables RNA helicase activity. Contributes to inositol hexakisphosphate binding activity. Involved in poly(A)+ mRNA export from nucleus; tRNA export from nucleus; and translational termination. Located in cellular bud tip; cytoplasmic stress granule; and nucleus. Part of nuclear pore cytoplasmic filaments. Orthologous to human DDX19A (DEAD-box helicase 19A); DDX19B (DEAD-box helicase 19B); and DDX25 (DEAD-box helicase 25). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See DBP5 in Genome Data Viewer

Location:: chromosome: XV

Exon count:: 1

Sequence:: Chromosome: XV; NC_001147.6 (414459..415907, complement)

Chromosome XV - NC_001147.6 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001147.6

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Gle1 is required for tRNA to stimulate Dbp5 ATPase activity in vitro and promote Dbp5-mediated tRNA export in vivo in Saccharomyces cerevisiae.
Title: Gle1 is required for tRNA to stimulate Dbp5 ATPase activity in vitro and promote Dbp5-mediated tRNA export in vivo in Saccharomyces cerevisiae.
The nucleoporin Gle1 activates DEAD-box protein 5 (Dbp5) by promoting ATP binding and accelerating rate limiting phosphate release.
Title: The nucleoporin Gle1 activates DEAD-box protein 5 (Dbp5) by promoting ATP binding and accelerating rate limiting phosphate release.
Emerging molecular functions and novel roles for the DEAD-box protein Dbp5/DDX19 in gene expression.
Title: Emerging molecular functions and novel roles for the DEAD-box protein Dbp5/DDX19 in gene expression.
Dbp5 associates with RNA-bound Mex67 and Nab2 and its localization at the nuclear pore complex is sufficient for mRNP export and cell viability.
Title: Dbp5 associates with RNA-bound Mex67 and Nab2 and its localization at the nuclear pore complex is sufficient for mRNP export and cell viability.
Dbp5 is thought to remove Mex67 from transcripts but does not affect the interaction of Mex67 with the nuclear pore complex
Title: The RNA export factor Mex67 functions as a mobile nucleoporin.
Disruptions in Dbp5 nucleocytoplasmic transport result in tRNA export defects, including changes in tRNA shuttling dynamics during recovery from nutrient stress.
Title: A nuclear role for the DEAD-box protein Dbp5 in tRNA export.
Defects in the Dbp5-guided eRF1 delivery lead to premature contact and premature dissociation of eRF1 and eRF3 from the ribosome and to subsequent stop codon readthrough. Thus, the stepwise Dbp5-controlled termination complex assembly is essential for regular translation termination events
Title: Translation termination depends on the sequential ribosomal entry of eRF1 and eRF3.
Dbp5 supports ribosomal transport by capturing ribosomal subunits upon their cytoplasmic appearance at the nuclear pore complex, possibly by binding export factors such as Mex67.
Title: Nuclear Export of Pre-Ribosomal Subunits Requires Dbp5, but Not as an RNA-Helicase as for mRNA Export.
These data show that ATP binds Dbp5 weakly in rapid equilibrium with a binding affinity (KT~4 mM) comparable to the KM for steady-state cycling, while ADP binds an order of magnitude more tightly (KD~0.4 mM).
Title: P(I) Release Limits the Intrinsic and RNA-Stimulated ATPase Cycles of DEAD-Box Protein 5 (Dbp5).
Gle1 specifically binds IP(6); this interaction is required for the full potentiation of Dbp5 ATPase activity during both mRNA export and translation termination
Title: Control of mRNA export and translation termination by inositol hexakisphosphate requires specific interaction with Gle1.

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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 ATP-dependent activity, acting on RNA	IDA Inferred from Direct Assay more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
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
contributes_to inositol hexakisphosphate binding	IDA Inferred from Direct Assay more info	PubMed
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 chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in mRNA export from nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA transport	IEA Inferred from Electronic Annotation more info
involved_in poly(A)+ mRNA export from nucleus	IBA Inferred from Biological aspect of Ancestor more info
involved_in poly(A)+ mRNA export from nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein transport	IEA Inferred from Electronic Annotation more info
involved_in tRNA export from nucleus	IDA Inferred from Direct Assay more info	PubMed
involved_in translational termination	IGI Inferred from Genetic Interaction more info	PubMed
involved_in translational termination	IPI Inferred from Physical Interaction more info	PubMed

Component	Evidence Code	Pubs
located_in cellular bud tip	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
is_active_in cytoplasmic stress granule	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasmic stress granule	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in nuclear membrane	IEA Inferred from Electronic Annotation more info
part_of nuclear pore	IEA Inferred from Electronic Annotation more info
part_of nuclear pore cytoplasmic filaments	IDA Inferred from Direct Assay more info	PubMed
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: ATP-dependent RNA helicase DBP5

NP_014689.1

EC 3.6.4.13

Cytoplasmic ATP-dependent RNA helicase of the DEAD-box family; involved in mRNA export from the nucleus, remodeling messenger ribonucleoprotein particles (mRNPs), with ATPase activity stimulated by Gle1p, IP6 and Nup159p; involved in translation termination along with Sup45p (eRF1); role in the cellular response to heat 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_001147.6 Reference assembly

Range

414459..415907 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001183465.1 → NP_014689.1 TPA: ATP-dependent RNA helicase DBP5 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_014689.1

Status: REVIEWED

UniProtKB/Swiss-Prot

A6ZNQ1, D6W2B2, P20449

UniProtKB/TrEMBL

B3LJ98, B5VRU5, C8ZI08, G2WMS7, N1NVR3

Conserved Domains (1) summary

COG0513
Location:64 → 481

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