MTR4 ATP-dependent RNA helicase MTR4 [Saccharomyces cerevisiae S288C] - Gene

Summary

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Official Symbol: MTR4
Official Full Name: ATP-dependent RNA helicase MTR4
Primary source: SGD:S000003586
Locus tag: YJL050W
See related: AllianceGenome:SGD:S000003586; FungiDB:YJL050W; VEuPathDB:YJL050W
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: DOB1
Summary: Enables 3'-5' RNA helicase activity and poly(A) binding activity. Involved in RNA metabolic process. Located in nucleolus. Part of TRAMP complex. Orthologous to human MTREX (Mtr4 exosome RNA helicase). [provided by Alliance of Genome Resources, Dec 2024]
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Genomic context

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See MTR4 in Genome Data Viewer

Location:: chromosome: X

Exon count:: 1

Sequence:: Chromosome: X; NC_001142.9 (342522..345743)

Chromosome X - NC_001142.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:: NC_001142.9

Go to nucleotide: Graphics FASTA GenBank

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Conserved Residues at the Mtr4 C-Terminus Coordinate Helicase Activity and Exosome Interactions.
Title: Conserved Residues at the Mtr4 C-Terminus Coordinate Helicase Activity and Exosome Interactions.
In vivo characterization of the critical interaction between the RNA exosome and the essential RNA helicase Mtr4 in Saccharomyces cerevisiae.
Title: In vivo characterization of the critical interaction between the RNA exosome and the essential RNA helicase Mtr4 in Saccharomyces cerevisiae.
Purification and characterization of Mtr4 and TRAMP from S. cerevisiae.
Title: Purification and characterization of Mtr4 and TRAMP from S. cerevisiae.
Hydrogen-deuterium exchange mass spectrometry of Mtr4 with diverse RNAs reveals substrate-dependent dynamics and interfaces in the arch.
Title: Hydrogen-deuterium exchange mass spectrometry of Mtr4 with diverse RNAs reveals substrate-dependent dynamics and interfaces in the arch.
Structure of the Maturing 90S Pre-ribosome in Association with the RNA Exosome.
Title: Structure of the Maturing 90S Pre-ribosome in Association with the RNA Exosome.
Mpp6-exosomes can recruit Mtr4, while Mpp6 and Rrp47 each contribute to Mtr4-dependent RNA decay, with maximal Mtr4-dependent decay observed with both cofactors.
Title: Structure and reconstitution of yeast Mpp6-nuclear exosome complexes reveals that Mpp6 stimulates RNA decay and recruits the Mtr4 helicase.
report the 3.2 A resolution crystal structure of S. cerevisiae Mtr4 bound to the interacting region of Nop53, revealing how the KOW domain of the helicase recognizes the AIM sequence of Nop53 with a network of hydrophobic and electrostatic interactions
Title: Structural insights into the interaction of the nuclear exosome helicase Mtr4 with the preribosomal protein Nop53.
Rrp41 mutations blocked substrate passage through the channel to Rrp44 only for cytoplasmic mRNAs, supporting the predicted widening of the lumen in the Rrp6-associated.Many exosome substrates exhibited clear preferences for a specific path to Rrp44. Both threading and direct access routes involve the RNA helicase Mtr4
Title: Transcriptome-wide analysis of alternative routes for RNA substrates into the exosome complex.
Mtr4p structural domain mutants in the helicase core reduced Mtr4p RNA binding, ATPase activity and unwinding activity in vitro.
Title: Mutations in Mtr4 Structural Domains Reveal Their Important Role in Regulating tRNAiMet Turnover in Saccharomyces cerevisiae and Mtr4p Enzymatic Activities In Vitro.
Study reports the identification of adaptor proteins that recruit the exosome-associated helicase, Mtr4, to unique RNA substrates. Nop53, the yeast homolog of the tumor suppressor PICT1, targets Mtr4 to pre-ribosomal particles for exosome-mediated processing, while a second adaptor Utp18 recruits Mtr4 to cleaved rRNA fragments destined for degradation by the exosome.
Title: The Exosome Is Recruited to RNA Substrates through Specific Adaptor Proteins.

Submit: New GeneRIF Correction See all GeneRIFs (21)

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 3'-5' RNA helicase activity	IDA Inferred from Direct Assay more info	PubMed
enables 3'-5' RNA helicase activity	IMP Inferred from Mutant Phenotype more info	PubMed
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 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	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
enables mRNA binding	HDA more info	PubMed
enables oxidoreductase activity	IEA Inferred from Electronic Annotation more info
enables poly(A) binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in RNA catabolic process	IEA Inferred from Electronic Annotation more info
involved_in TRAMP-dependent tRNA surveillance pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in TRAMP-dependent tRNA surveillance pathway	IGI Inferred from Genetic Interaction more info	PubMed
involved_in U4 snRNA 3'-end processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in U5 snRNA 3'-end processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in exonucleolytic trimming to generate mature 3'-end 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 mRNA processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in maturation of 5.8S rRNA	IBA Inferred from Biological aspect of Ancestor more info
involved_in nuclear mRNA surveillance	IGI Inferred from Genetic Interaction more info	PubMed
involved_in nuclear mRNA surveillance of mRNA 3'-end processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear polyadenylation-dependent mRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear polyadenylation-dependent rRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in poly(A)-dependent snoRNA 3'-end processing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in rRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in rRNA processing	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of TRAMP complex	IBA Inferred from Biological aspect of Ancestor more info
part_of TRAMP complex	IDA Inferred from Direct Assay more info	PubMed
part_of TRAMP complex	IPI Inferred from Physical Interaction more info	PubMed
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
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 MTR4

NP_012485.1

EC 3.6.4.13

RNA duplex-sensing translocase; ATP-dependent 3'-5' RNA helicase of the DExD/H family; involved in nuclear RNA processing and degradation as a component of TRAMP complex and in TRAMP-independent processes; TRAMP unwinds RNA duplexes, with Mtr4p unwinding activity stimulated by Pap2p/Air2p but not dependent on ongoing polyadenylation; contains an arch domain, with two coiled-coil arms/stalks and a globular fist/KOW domain, which has RNA binding activity and is required for 5.8S rRNA processing

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_001142.9 Reference assembly

Range

342522..345743

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001181483.1 → NP_012485.1 TPA: ATP-dependent RNA helicase MTR4 [Saccharomyces cerevisiae S288C]

See identical proteins and their annotated locations for NP_012485.1

Status: REVIEWED

UniProtKB/Swiss-Prot

D6VWD3, P47047

UniProtKB/TrEMBL

G2WGW7, N1P364

Conserved Domains (1) summary

COG4581
Location:21 → 1073

Dob10; Superfamily II RNA helicase [Replication, recombination and repair]