DBP2 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: DBP2
Primary source: SGD:S000005056
Locus tag: YNL112W
See related: AllianceGenome:SGD:S000005056; FungiDB:YNL112W; VEuPathDB:YNL112W
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; mRNA binding activity; and snoRNA binding activity. Involved in RNA metabolic process and messenger ribonucleoprotein complex assembly. Located in nucleus. Used to study abdominal obesity-metabolic syndrome and cancer. Orthologous to several human genes including DDX17 (DEAD-box helicase 17). [provided by Alliance of Genome Resources, Apr 2022]
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Genomic context

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Location:: chromosome: XIV

Exon count:: 2

Sequence:: Chromosome: XIV; NC_001146.8 (413639..416281)

Chromosome XIV - NC_001146.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001146.8

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Nonstructural N- and C-tails of Dbp2 confer the protein full helicase activities.
Title: Nonstructural N- and C-tails of Dbp2 confer the protein full helicase activities.
DEAD-box RNA helicase Dbp2 binds to G-quadruplex nucleic acids and regulates different conformation of G-quadruplex DNA.
Title: DEAD-box RNA helicase Dbp2 binds to G-quadruplex nucleic acids and regulates different conformation of G-quadruplex DNA.
Dbp2 in S. cerevisiae remodels secondary structures within the 39 ends of a subset of mRNAs to promote efficient termination by the Nrd1-Nab3-Sen1 (NNS) complex.
Title: Genome-Wide Discovery of DEAD-Box RNA Helicase Targets Reveals RNA Structural Remodeling in Transcription Termination.
our data link Dbp2p to noncoding RNAs, Sen1p, and R-loops. The transcriptome-wide connection to R-loops provides a unifying theme for diverse cellular roles of Dbp2p
Title: The DEAD-box protein Dbp2p is linked to noncoding RNAs, the helicase Sen1p, and R-loops.
Dbp2 integrates nutrient availability with energy homeostasis by maintaining repression of glucose-repressed, Cyc8-targeted genes across the genome.
Title: Metabolic Adaptation to Nutrients Involves Coregulation of Gene Expression by the RNA Helicase Dbp2 and the Cyc8 Corepressor in Saccharomyces cerevisiae.
Results show refined biochemical and biological comparison of yeast Dbp2 and human DDX5 enzymes. Human DDX5 possesses a 10-fold higher unwinding activity than Dbp2, partially due to the presence of a mammalian/avian specific C-terminal extension. Also, ectopic expression of DDX5 rescues the cold sensitivity, cryptic initiation defects, and impaired glucose import in dbp2Delta cells, suggesting functional conservation.
Title: Characterization of the mammalian DEAD-box protein DDX5 reveals functional conservation with S. cerevisiae ortholog Dbp2 in transcriptional control and glucose metabolism.
These data show that Yra1 inhibits unwinding in a concentration-dependent manner by preventing the association of Dbp2 with single-stranded RNA.
Title: Recruitment, Duplex Unwinding and Protein-Mediated Inhibition of the Dead-Box RNA Helicase Dbp2 at Actively Transcribed Chromatin.
Dbp2 is a missing link in RNA quality control that functions to maintain the fidelity of transcriptional processes.
Title: The DEAD-box RNA helicase Dbp2 connects RNA quality control with repression of aberrant transcription.

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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 activity, acting on RNA	IDA Inferred from Direct Assay more info	PubMed
enables ATP-dependent activity, acting on RNA	IMP Inferred from Mutant Phenotype more info	PubMed
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 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 mRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables nucleic acid binding	IEA Inferred from Electronic Annotation more info
enables snoRNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in alternative mRNA splicing, via spliceosome	IBA Inferred from Biological aspect of Ancestor more info
involved_in gene expression	IEA Inferred from Electronic Annotation more info
involved_in nuclear polyadenylation-dependent mRNA catabolic process	IGI Inferred from Genetic Interaction more info	PubMed
involved_in nuclear polyadenylation-dependent mRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IEA Inferred from Electronic Annotation more info
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IPI Inferred from Physical Interaction more info	PubMed
involved_in rRNA processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in rRNA processing	IEA Inferred from Electronic Annotation more info
involved_in rRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ribosome biogenesis	IEA Inferred from Electronic Annotation more info
involved_in termination of RNA polymerase II transcription	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	HDA more info	PubMed
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in mitochondrion	HDA more info	PubMed
located_in nucleus	HDA 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
part_of ribonucleoprotein complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: DEAD-box ATP-dependent RNA helicase DBP2

NP_014287.3

EC 3.6.4.13

ATP-dependent RNA helicase of the DEAD-box protein family; has strong preference for dsRNA; remodels RNA-protein complex (RNP) to facilitate efficient transcription termination; required for assembly of Yra1p, Nab2p and Mex67p onto mRNA and formation of nuclear mRNP; involved in mRNA decay and rRNA processing; may be involved in suppression of transcription from cryptic initiation sites

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_001146.8 Reference assembly

Range

413639..416281

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001182950.3 → NP_014287.3 TPA: DEAD-box ATP-dependent RNA helicase DBP2 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_014287.3

Status: REVIEWED

UniProtKB/Swiss-Prot

A6ZRX0, D6W169, P24783, Q05456

UniProtKB/TrEMBL

B3LNW9, C8ZGB8, G2WLZ4

Conserved Domains (1) summary

PTZ00110
Location:4 → 492

PTZ00110; helicase; Provisional