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YEAST:MTR4
Contents
| Species (Taxon ID) | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast). (559292) | |
| Gene Name(s) | MTR4 (synonyms: DOB1) | |
| Protein Name(s) | ATP-dependent RNA helicase DOB1
mRNA transport regulator MTR4 | |
| External Links | ||
| UniProt | P47047 | |
| EMBL | Z49325 BK006943 | |
| PIR | S56822 | |
| RefSeq | NP_012485.1 | |
| PDB | 2XGJ 4QU4 4U4C 4WFD | |
| PDBsum | 2XGJ 4QU4 4U4C 4WFD | |
| ProteinModelPortal | P47047 | |
| SMR | P47047 | |
| BioGrid | 33705 | |
| DIP | DIP-6394N | |
| IntAct | P47047 | |
| MINT | MINT-620894 | |
| iPTMnet | P47047 | |
| MaxQB | P47047 | |
| PeptideAtlas | P47047 | |
| EnsemblFungi | YJL050W | |
| GeneID | 853397 | |
| KEGG | sce:YJL050W | |
| EuPathDB | FungiDB:YJL050W | |
| SGD | S000003586 | |
| GeneTree | ENSGT00820000127042 | |
| HOGENOM | HOG000163047 | |
| InParanoid | P47047 | |
| KO | K12598 | |
| OMA | HDVSYPE | |
| OrthoDB | EOG7WT48P | |
| BioCyc | YEAST:G3O-31514-MONOMER | |
| BRENDA | 3.6.4.13 | |
| Reactome | [www.reactome.org/content/detail/R-SCE-6791226 R-SCE-6791226] | |
| EvolutionaryTrace | P47047 | |
| PRO | PR:P47047 | |
| Proteomes | UP000002311 | |
| GO | GO:0005730 GO:0005634 GO:0031499 GO:0005524 GO:0034459 GO:0016491 GO:0008143 GO:0000467 GO:0043629 GO:0071031 GO:0071042 GO:0071035 GO:0071038 GO:0071049 GO:0071051 GO:0016075 GO:0034475 GO:0034476 | |
| Gene3D | 3.40.50.300 | |
| InterPro | IPR011545 IPR014001 IPR001650 IPR027417 IPR011254 IPR025696 IPR016438 IPR012961 | |
| Pfam | PF00270 PF08148 PF00271 PF13234 | |
| PIRSF | PIRSF005198 | |
| SMART | SM00487 SM01142 SM00490 | |
| SUPFAM | SSF52540 SSF56821 | |
| PROSITE | PS51192 PS51194 | |
Annotations
| Qualifier | GO ID | GO term name | Reference | ECO ID | ECO term name | with/from | Aspect | Extension | Notes | Status |
|---|---|---|---|---|---|---|---|---|---|---|
| GO:0000292 |
RNA fragment catabolic process |
ECO:0000315 |
P |
RNA polymerase I produces pre-rRNA that is processed into several fragments, including the 5’-ETS (external transcribed spacer) and 7S pre-rRNA. The RNA exosome is a 3’ to 5’ exonuclease involved in the processing of 7S pre-rRNA into mature 5.8S rRNA and in the degradation of the 5’-ETS. The exosome requires protein cofactors that interact with the Mtr4 helicase for substrate specificity. Figure 1 F is a northern blot that shows that S. cerevisiae strains with a deletion in Mtr4’s essential arch domain accumulate 5’-ETS (lane 2). A wilde type Mtr4 strain shows that 5’ETS is degraded as it is absent on the northern blot (lane 1). Therefore, lanes 1 and 2 show that Mtr4 is involved in the breakdown of a fragment of RNA, such as excised introns or sequences removed from ribosomal RNA during processing (Go termGO:0000292) |
complete | |||||
| GO:0000460 |
maturation of 5.8S rRNA |
ECO:0000315 |
P |
RNA polymerase I produces pre-rRNA that is processed into several fragments, including the 5’-ETS (external transcribed spacer) and 7S pre-rRNA. The RNA exosome is a 3’ to 5’ exonuclease involved in the processing of 7S pre-rRNA into mature 5.8S rRNA and in the degradation of the 5’-ETS. The exosome requires protein cofactors that interact with the Mtr4 helicase for substrate specificity. One of these cofactors is Nop53. The N-terminus of Nop53 is required for binding with the arch domain of Mtr4, and subsequently for presentation of the 7S pre-rRNA substrate to the RNA exosome. The northern blot in Figure 1 shows that S. cerevisiae strains with wild type Mtr4 and Nop53 accumulate no 7S-pre-rRNA. Conversely, mutants with a deletion in either the arch domain of Mtr4 or the N terminus of Nop53 show accumulation of 7S-pre-rRNA. Therefore these two proteins are involved in he maturation of a precursor 5.8S ribosomal RNA (rRNA) molecule into a mature 5.8S rRNA molecule (GO:0000460) |
complete | |||||
|
enables |
GO:0003729 |
mRNA binding |
ECO:0007005 |
high throughput direct assay evidence used in manual assertion |
F |
Seeded From UniProt |
complete | |||
|
involved_in |
GO:0016973 |
poly(A)+ mRNA export from nucleus |
ECO:0000315 |
mutant phenotype evidence used in manual assertion |
P |
Seeded From UniProt |
complete | |||
|
involved_in |
GO:0071051 |
polyadenylation-dependent snoRNA 3'-end processing |
ECO:0000315 |
mutant phenotype evidence used in manual assertion |
P |
Seeded From UniProt |
complete | |||
|
involved_in |
GO:0071049 |
nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription |
ECO:0000316 |
genetic interaction evidence used in manual assertion |
SGD:S000001377 |
P |
Seeded From UniProt |
complete | ||
|
involved_in |
GO:0071042 |
nuclear polyadenylation-dependent mRNA catabolic process |
ECO:0000315 |
mutant phenotype evidence used in manual assertion |
P |
Seeded From UniProt |
complete | |||
|
involved_in |
GO:0071038 |
nuclear polyadenylation-dependent tRNA catabolic process |
ECO:0000316 |
genetic interaction evidence used in manual assertion |
SGD:S000005006 |
P |
Seeded From UniProt |
complete | ||
|
involved_in |
GO:0071038 |
nuclear polyadenylation-dependent tRNA catabolic process |
ECO:0000314 |
direct assay evidence used in manual assertion |
P |
Seeded From UniProt |
complete | |||
|
involved_in |
GO:0071038 |
nuclear polyadenylation-dependent tRNA catabolic process |
ECO:0000314 |
direct assay evidence used in manual assertion |
P |
Seeded From UniProt |
complete | |||
|
involved_in |
GO:0071038 |
nuclear polyadenylation-dependent tRNA catabolic process |
ECO:0000314 |
direct assay evidence used in manual assertion |
P |
Seeded From UniProt |
complete | |||
|
involved_in |
GO:0071035 |
nuclear polyadenylation-dependent rRNA catabolic process |
ECO:0000315 |
mutant phenotype evidence used in manual assertion |
P |
Seeded From UniProt |
complete | |||
|
involved_in |
GO:0071035 |
nuclear polyadenylation-dependent rRNA catabolic process |
ECO:0000315 |
mutant phenotype evidence used in manual assertion |
P |
Seeded From UniProt |
complete | |||
|
involved_in |
GO:0071031 |
nuclear mRNA surveillance of mRNA 3'-end processing |
ECO:0000316 |
genetic interaction evidence used in manual assertion |
P |
Seeded From UniProt |
Missing: with/from | |||
|
involved_in |
GO:0071031 |
nuclear mRNA surveillance of mRNA 3'-end processing |
ECO:0000315 |
mutant phenotype evidence used in manual assertion |
P |
Seeded From UniProt |
complete | |||
|
involved_in |
GO:0043629 |
ncRNA polyadenylation |
ECO:0000314 |
direct assay evidence used in manual assertion |
P |
Seeded From UniProt |
complete | |||
|
involved_in |
GO:0043629 |
ncRNA polyadenylation |
ECO:0000314 |
direct assay evidence used in manual assertion |
P |
Seeded From UniProt |
complete | |||
|
involved_in |
GO:0034476 |
U5 snRNA 3'-end processing |
ECO:0000315 |
mutant phenotype evidence used in manual assertion |
P |
Seeded From UniProt |
complete | |||
|
involved_in |
GO:0034475 |
U4 snRNA 3'-end processing |
ECO:0000315 |
mutant phenotype evidence used in manual assertion |
P |
Seeded From UniProt |
complete | |||
|
involved_in |
GO:0034475 |
U4 snRNA 3'-end processing |
ECO:0000315 |
mutant phenotype evidence used in manual assertion |
P |
Seeded From UniProt |
complete | |||
|
enables |
GO:0034459 |
ATP-dependent 3'-5' RNA helicase activity |
ECO:0000315 |
mutant phenotype evidence used in manual assertion |
F |
Seeded From UniProt |
complete | |||
|
enables |
GO:0034459 |
ATP-dependent 3'-5' RNA helicase activity |
ECO:0000314 |
direct assay evidence used in manual assertion |
F |
Seeded From UniProt |
complete | |||
|
enables |
GO:0034459 |
ATP-dependent 3'-5' RNA helicase activity |
ECO:0000314 |
direct assay evidence used in manual assertion |
F |
Seeded From UniProt |
complete | |||
|
part_of |
GO:0031499 |
TRAMP complex |
ECO:0000353 |
physical interaction evidence used in manual assertion |
SGD:S000005475 |
C |
Seeded From UniProt |
complete | ||
|
part_of |
GO:0031499 |
TRAMP complex |
ECO:0000314 |
direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
|
part_of |
GO:0031499 |
TRAMP complex |
ECO:0000314 |
direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
|
part_of |
GO:0031499 |
TRAMP complex |
ECO:0000314 |
direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
|
involved_in |
GO:0016075 |
rRNA catabolic process |
ECO:0000315 |
mutant phenotype evidence used in manual assertion |
P |
Seeded From UniProt |
complete | |||
|
involved_in |
GO:0016075 |
rRNA catabolic process |
ECO:0000315 |
mutant phenotype evidence used in manual assertion |
P |
Seeded From UniProt |
complete | |||
|
enables |
GO:0008143 |
poly(A) binding |
ECO:0000314 |
direct assay evidence used in manual assertion |
F |
Seeded From UniProt |
complete | |||
|
part_of |
GO:0005730 |
nucleolus |
ECO:0000314 |
direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
|
part_of |
GO:0005634 |
nucleus |
ECO:0000314 |
direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
|
part_of |
GO:0005634 |
nucleus |
ECO:0000314 |
direct assay evidence used in manual assertion |
C |
Seeded From UniProt |
complete | |||
|
involved_in |
GO:0000467 |
exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) |
ECO:0000315 |
mutant phenotype evidence used in manual assertion |
P |
Seeded From UniProt |
complete | |||
|
involved_in |
GO:0000467 |
exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) |
ECO:0000315 |
mutant phenotype evidence used in manual assertion |
P |
Seeded From UniProt |
complete | |||
|
involved_in |
GO:0006401 |
RNA catabolic process |
ECO:0000318 |
biological aspect of ancestor evidence used in manual assertion |
PANTHER:PTN002281432 |
P |
Seeded From UniProt |
complete | ||
|
part_of |
GO:0005634 |
nucleus |
ECO:0000318 |
biological aspect of ancestor evidence used in manual assertion |
PANTHER:PTN002281442 |
C |
Seeded From UniProt |
complete | ||
|
enables |
GO:0004004 |
ATP-dependent RNA helicase activity |
ECO:0000318 |
biological aspect of ancestor evidence used in manual assertion |
PANTHER:PTN002281432 |
F |
Seeded From UniProt |
complete | ||
|
involved_in |
GO:0000460 |
maturation of 5.8S rRNA |
ECO:0000318 |
biological aspect of ancestor evidence used in manual assertion |
PANTHER:PTN002281442 |
P |
Seeded From UniProt |
complete | ||
|
enables |
GO:0003676 |
nucleic acid binding |
ECO:0000256 |
match to sequence model evidence used in automatic assertion |
F |
Seeded From UniProt |
complete | |||
|
enables |
GO:0003723 |
RNA binding |
ECO:0000256 |
match to sequence model evidence used in automatic assertion |
F |
Seeded From UniProt |
complete | |||
|
enables |
GO:0003724 |
RNA helicase activity |
ECO:0000256 |
match to sequence model evidence used in automatic assertion |
F |
Seeded From UniProt |
complete | |||
|
enables |
GO:0003824 |
catalytic activity |
ECO:0000256 |
match to sequence model evidence used in automatic assertion |
F |
Seeded From UniProt |
complete | |||
|
enables |
GO:0005524 |
ATP binding |
ECO:0000256 |
match to sequence model evidence used in automatic assertion |
F |
Seeded From UniProt |
complete | |||
|
involved_in |
GO:0006401 |
RNA catabolic process |
ECO:0000256 |
match to sequence model evidence used in automatic assertion |
P |
Seeded From UniProt |
complete | |||
|
enables |
GO:0016491 |
oxidoreductase activity |
ECO:0000256 |
match to sequence model evidence used in automatic assertion |
F |
Seeded From UniProt |
complete | |||
|
involved_in |
GO:0055114 |
oxidation-reduction process |
ECO:0000256 |
match to sequence model evidence used in automatic assertion |
P |
Seeded From UniProt |
complete | |||
|
part_of |
GO:0005634 |
nucleus |
ECO:0000322 |
imported manually asserted information used in automatic assertion |
C |
Seeded From UniProt |
complete | |||
|
enables |
GO:0005524 |
ATP binding |
ECO:0000322 |
imported manually asserted information used in automatic assertion |
F |
Seeded From UniProt |
complete | |||
|
involved_in |
GO:0006364 |
rRNA processing |
ECO:0000322 |
imported manually asserted information used in automatic assertion |
P |
Seeded From UniProt |
complete | |||
|
enables |
GO:0016787 |
hydrolase activity |
ECO:0000322 |
imported manually asserted information used in automatic assertion |
F |
Seeded From UniProt |
complete | |||
|
enables |
GO:0000166 |
nucleotide binding |
ECO:0000322 |
imported manually asserted information used in automatic assertion |
F |
Seeded From UniProt |
complete | |||
|
enables |
GO:0004386 |
helicase activity |
ECO:0000322 |
imported manually asserted information used in automatic assertion |
F |
Seeded From UniProt |
complete | |||
Notes
References
See Help:References for how to manage references in GONUTS.
- ↑ 1.0 1.1 Thoms, M et al. (2015) The Exosome Is Recruited to RNA Substrates through Specific Adaptor Proteins. Cell 162 1029-38 PubMed GONUTS page
- ↑ Mitchell, SF et al. (2013) Global analysis of yeast mRNPs. Nat. Struct. Mol. Biol. 20 127-33 PubMed GONUTS page
- ↑ Paul, B & Montpetit, B (2016) Altered RNA processing and export lead to retention of mRNAs near transcription sites and nuclear pore complexes or within the nucleolus. Mol. Biol. Cell 27 2742-56 PubMed GONUTS page
- ↑ 4.0 4.1 van Hoof, A et al. (2000) Yeast exosome mutants accumulate 3'-extended polyadenylated forms of U4 small nuclear RNA and small nucleolar RNAs. Mol. Cell. Biol. 20 441-52 PubMed GONUTS page
- ↑ Hilleren, P et al. (2001) Quality control of mRNA 3'-end processing is linked to the nuclear exosome. Nature 413 538-42 PubMed GONUTS page
- ↑ Roth, KM et al. (2009) Regulation of NAB2 mRNA 3'-end formation requires the core exosome and the Trf4p component of the TRAMP complex. RNA 15 1045-58 PubMed GONUTS page
- ↑ 7.0 7.1 7.2 Wang, X et al. (2008) Degradation of hypomodified tRNA(iMet) in vivo involves RNA-dependent ATPase activity of the DExH helicase Mtr4p. RNA 14 107-16 PubMed GONUTS page
- ↑ Schneider, C et al. (2007) The exosome subunit Rrp44 plays a direct role in RNA substrate recognition. Mol. Cell 27 324-31 PubMed GONUTS page
- ↑ 9.0 9.1 9.2 Vanácová, S et al. (2005) A new yeast poly(A) polymerase complex involved in RNA quality control. PLoS Biol. 3 e189 PubMed GONUTS page
- ↑ 10.0 10.1 10.2 LaCava, J et al. (2005) RNA degradation by the exosome is promoted by a nuclear polyadenylation complex. Cell 121 713-24 PubMed GONUTS page
- ↑ Callahan, KP & Butler, JS (2008) Evidence for core exosome independent function of the nuclear exoribonuclease Rrp6p. Nucleic Acids Res. 36 6645-55 PubMed GONUTS page
- ↑ Houseley, J & Tollervey, D (2006) Yeast Trf5p is a nuclear poly(A) polymerase. EMBO Rep. 7 205-11 PubMed GONUTS page
- ↑ 13.0 13.1 Rougemaille, M et al. (2007) Dissecting mechanisms of nuclear mRNA surveillance in THO/sub2 complex mutants. EMBO J. 26 2317-26 PubMed GONUTS page
- ↑ 14.0 14.1 14.2 14.3 Allmang, C et al. (1999) Functions of the exosome in rRNA, snoRNA and snRNA synthesis. EMBO J. 18 5399-410 PubMed GONUTS page
- ↑ 15.0 15.1 Bernstein, J et al. (2008) Characterization of the essential activities of Saccharomyces cerevisiae Mtr4p, a 3'->5' helicase partner of the nuclear exosome. J. Biol. Chem. 283 4930-42 PubMed GONUTS page
- ↑ 16.0 16.1 Wyers, F et al. (2005) Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase. Cell 121 725-37 PubMed GONUTS page
- ↑ 17.0 17.1 de la Cruz, J et al. (1998) Dob1p (Mtr4p) is a putative ATP-dependent RNA helicase required for the 3' end formation of 5.8S rRNA in Saccharomyces cerevisiae. EMBO J. 17 1128-40 PubMed GONUTS page
- ↑ Dez, C et al. (2006) Surveillance of nuclear-restricted pre-ribosomes within a subnucleolar region of Saccharomyces cerevisiae. EMBO J. 25 1534-46 PubMed GONUTS page
- ↑ Pertschy, B et al. (2004) Diazaborine treatment of yeast cells inhibits maturation of the 60S ribosomal subunit. Mol. Cell. Biol. 24 6476-87 PubMed GONUTS page
- ↑ Liang, S et al. (1996) A DEAD-box-family protein is required for nucleocytoplasmic transport of yeast mRNA. Mol. Cell. Biol. 16 5139-46 PubMed GONUTS page
- ↑ 21.0 21.1 21.2 21.3 Gaudet, P et al. (2011) Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Brief. Bioinformatics 12 449-62 PubMed GONUTS page
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- GO:0071031 ! nuclear mRNA surveillance of mRNA 3'-end processing
- GO:0071042 ! nuclear polyadenylation-dependent mRNA catabolic process
- GO:0071035 ! nuclear polyadenylation-dependent rRNA catabolic process
- GO:0071049 ! nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription
- GO:0003676 ! nucleic acid binding
- GO:0005730 ! nucleolus
- GO:0000166 ! nucleotide binding
- GO:0005634 ! nucleus
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