gtpbp3 encodes a mitochondrial GTPase subunit of the GTPBP3-MTO1 complex required for taurine-containing wobble uridine (tau-5-methyluridine) modification of mitochondrial tRNAs. Its GTPase activity drives this tRNA modification; loss impairs mitochondrial translation, with reduced mitochondrial tRNA aminoacylation arising as a downstream consequence rather than from a direct aminoacyl-tRNA ligase activity of the protein.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | REMOVE | Summary: cytoplasm (GO:0005737) is too coarse for gtpbp3, whose specific mitochondrion location is annotated separately. Reason: gtpbp3 is a mitochondrial tRNA-modifying enzyme. Mitochondrion (GO:0005739) is part_of cytoplasm and is annotated directly for this gene, so the transferred cytoplasm term is a true-but-uninformative parent and is removed as redundant rather than retained. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000182687 Β· GTPBP3/MnmE tRNA-modifying GTPase family node SUPPORTS TRANSFER gtpbp3 is a mitochondrial tRNA-modifying enzyme. GO defines mitochondrion (GO:0005739) as part_of cytoplasm, so the transferred cytoplasm term is technically true but too coarse; it is removed as redundant with the specific mitochondrion annotation reviewed separately. SGD:S000004625 Β· yeast MSS1 mitochondrial GTPase donor SUPPORTS TRANSFER Donor supports the localization; the specific mitochondrion term supersedes the vague cytoplasm parent for this gene. Supporting Evidence: file:DANRE/gtpbp3/gtpbp3-uniprot.txt the 5-taurinomethyluridine (taum(5)U) modification at the 34th wobble position PMID:30916346 GTPBP3 is a highly conserved tRNA modifying enzyme for the biosynthesis of Οm5U at the wobble position of mitochondrial tRNA |
| GO:0002098 tRNA wobble uridine modification | IBA GO_REF:0000033 | ACCEPT | Summary: tRNA wobble uridine modification (GO:0002098) is supported for gtpbp3. Reason: This annotation matches the synthesized core function or a directly supported core location/process for this gene. Supporting Evidence: file:DANRE/gtpbp3/gtpbp3-uniprot.txt the 5-taurinomethyluridine (taum(5)U) modification at the 34th wobble position PMID:30916346 GTPBP3 is a highly conserved tRNA modifying enzyme for the biosynthesis of Οm5U at the wobble position of mitochondrial tRNA file:DANRE/gtpbp3/gtpbp3-deep-research-falcon.md Across mechanistic summaries, GTPBP3 functions together with MTO1 in the **biosynthesis of Οm5U/Οm5(s2)U at mitochondrial tRNA wobble uridine (U34)** |
| GO:0005739 mitochondrion | IBA GO_REF:0000033 | ACCEPT | Summary: mitochondrion (GO:0005739) is supported for gtpbp3. Reason: This annotation matches the synthesized core function or a directly supported core location/process for this gene. Supporting Evidence: file:DANRE/gtpbp3/gtpbp3-uniprot.txt the 5-taurinomethyluridine (taum(5)U) modification at the 34th wobble position PMID:30916346 GTPBP3 is a highly conserved tRNA modifying enzyme for the biosynthesis of Οm5U at the wobble position of mitochondrial tRNA |
| GO:0030488 tRNA methylation | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: tRNA methylation (GO:0030488) is retained as supported context for gtpbp3 but is not the primary/core function. Reason: This annotation is broad, inferred, or reflects downstream developmental/physiological context rather than the central molecular role. Supporting Evidence: file:DANRE/gtpbp3/gtpbp3-uniprot.txt the 5-taurinomethyluridine (taum(5)U) modification at the 34th wobble position PMID:30916346 GTPBP3 is a highly conserved tRNA modifying enzyme for the biosynthesis of Οm5U at the wobble position of mitochondrial tRNA |
| GO:0003924 GTPase activity | IEA GO_REF:0000002 | ACCEPT | Summary: GTPase activity (GO:0003924) is supported for gtpbp3. Reason: This annotation matches the synthesized core function or a directly supported core location/process for this gene. Supporting Evidence: file:DANRE/gtpbp3/gtpbp3-uniprot.txt the 5-taurinomethyluridine (taum(5)U) modification at the 34th wobble position PMID:30916346 GTPBP3 is a highly conserved tRNA modifying enzyme for the biosynthesis of Οm5U at the wobble position of mitochondrial tRNA file:DANRE/gtpbp3/gtpbp3-deep-research-falcon.md GTPBP3 is described as a **nuclear-encoded mitochondrial tRNA-modifying enzyme** with an **atypical TrmE-type GTPase** domain where **GTP hydrolysis is functionally important** |
| GO:0005525 GTP binding | IEA GO_REF:0000002 | ACCEPT | Summary: GTP binding (GO:0005525) is supported for gtpbp3. Reason: This annotation matches the synthesized core function or a directly supported core location/process for this gene. Supporting Evidence: file:DANRE/gtpbp3/gtpbp3-uniprot.txt the 5-taurinomethyluridine (taum(5)U) modification at the 34th wobble position PMID:30916346 GTPBP3 is a highly conserved tRNA modifying enzyme for the biosynthesis of Οm5U at the wobble position of mitochondrial tRNA |
| GO:0005739 mitochondrion | IEA GO_REF:0000120 | ACCEPT | Summary: mitochondrion (GO:0005739) is supported for gtpbp3. Reason: This annotation matches the synthesized core function or a directly supported core location/process for this gene. Supporting Evidence: file:DANRE/gtpbp3/gtpbp3-uniprot.txt the 5-taurinomethyluridine (taum(5)U) modification at the 34th wobble position PMID:30916346 GTPBP3 is a highly conserved tRNA modifying enzyme for the biosynthesis of Οm5U at the wobble position of mitochondrial tRNA |
| GO:0006400 tRNA modification | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: tRNA modification (GO:0006400) is retained as supported context for gtpbp3 but is not the primary/core function. Reason: This annotation is broad, inferred, or reflects downstream developmental/physiological context rather than the central molecular role. Supporting Evidence: file:DANRE/gtpbp3/gtpbp3-uniprot.txt the 5-taurinomethyluridine (taum(5)U) modification at the 34th wobble position PMID:30916346 GTPBP3 is a highly conserved tRNA modifying enzyme for the biosynthesis of Οm5U at the wobble position of mitochondrial tRNA |
| GO:0070900 mitochondrial tRNA modification | IEA GO_REF:0000117 | ACCEPT | Summary: mitochondrial tRNA modification (GO:0070900) is supported for gtpbp3. Reason: This annotation matches the synthesized core function or a directly supported core location/process for this gene. Supporting Evidence: file:DANRE/gtpbp3/gtpbp3-uniprot.txt the 5-taurinomethyluridine (taum(5)U) modification at the 34th wobble position PMID:30916346 GTPBP3 is a highly conserved tRNA modifying enzyme for the biosynthesis of Οm5U at the wobble position of mitochondrial tRNA |
| GO:0003924 GTPase activity | ISS GO_REF:0000024 | ACCEPT | Summary: GTPase activity (GO:0003924) is supported for gtpbp3. Reason: This annotation matches the synthesized core function or a directly supported core location/process for this gene. Supporting Evidence: file:DANRE/gtpbp3/gtpbp3-uniprot.txt the 5-taurinomethyluridine (taum(5)U) modification at the 34th wobble position PMID:30916346 GTPBP3 is a highly conserved tRNA modifying enzyme for the biosynthesis of Οm5U at the wobble position of mitochondrial tRNA |
| GO:0005739 mitochondrion | ISS GO_REF:0000024 | ACCEPT | Summary: mitochondrion (GO:0005739) is supported for gtpbp3. Reason: This annotation matches the synthesized core function or a directly supported core location/process for this gene. Supporting Evidence: file:DANRE/gtpbp3/gtpbp3-uniprot.txt the 5-taurinomethyluridine (taum(5)U) modification at the 34th wobble position PMID:30916346 GTPBP3 is a highly conserved tRNA modifying enzyme for the biosynthesis of Οm5U at the wobble position of mitochondrial tRNA |
| GO:0070899 mitochondrial tRNA wobble uridine modification | ISS GO_REF:0000024 | ACCEPT | Summary: mitochondrial tRNA wobble uridine modification (GO:0070899) is supported for gtpbp3. Reason: This annotation matches the synthesized core function or a directly supported core location/process for this gene. Supporting Evidence: file:DANRE/gtpbp3/gtpbp3-uniprot.txt the 5-taurinomethyluridine (taum(5)U) modification at the 34th wobble position PMID:30916346 GTPBP3 is a highly conserved tRNA modifying enzyme for the biosynthesis of Οm5U at the wobble position of mitochondrial tRNA file:DANRE/gtpbp3/gtpbp3-deep-research-falcon.md Across mechanistic summaries, GTPBP3 functions together with MTO1 in the **biosynthesis of Οm5U/Οm5(s2)U at mitochondrial tRNA wobble uridine (U34)** |
| GO:0036416 tRNA stabilization | IMP PMID:30916346 Deletion of Gtpbp3 in zebrafish revealed the hypertrophic ca... | KEEP AS NON CORE | Summary: tRNA stabilization (GO:0036416) is retained as supported context for gtpbp3 but is not the primary/core function. Reason: This annotation is broad, inferred, or reflects downstream developmental/physiological context rather than the central molecular role. Supporting Evidence: PMID:30916346 GTPBP3 is a highly conserved tRNA modifying enzyme for the biosynthesis of Οm5U at the wobble position of mitochondrial tRNA |
| GO:0070143 mitochondrial alanyl-tRNA aminoacylation | IMP PMID:30916346 Deletion of Gtpbp3 in zebrafish revealed the hypertrophic ca... | MARK AS OVER ANNOTATED | Summary: mitochondrial alanyl-tRNA aminoacylation (GO:0070143) likely overstates or misdirects the direct function of gtpbp3. Reason: The evidence is better explained by the gene core function (wobble U34 modification) or downstream phenotype; this term should not be treated as a direct/core annotation. The falcon synthesis reinforces this: gtpbp3-knockout zebrafish showed increased (not abolished) tRNA aminoacylation efficiencies, which is inconsistent with gtpbp3 acting as a direct aminoacyl-tRNA ligase and instead reflects an indirect consequence of altered tRNA modification. Supporting Evidence: PMID:30916346 GTPBP3 is a highly conserved tRNA modifying enzyme for the biosynthesis of Οm5U at the wobble position of mitochondrial tRNA file:DANRE/gtpbp3/gtpbp3-deep-research-falcon.md gtpbp3KO zebrafish showed increased efficiencies of tRNA aminoacylation |
| GO:0070153 mitochondrial leucyl-tRNA aminoacylation | IMP PMID:30916346 Deletion of Gtpbp3 in zebrafish revealed the hypertrophic ca... | MARK AS OVER ANNOTATED | Summary: mitochondrial leucyl-tRNA aminoacylation (GO:0070153) likely overstates or misdirects the direct function of gtpbp3. Reason: The evidence is better explained by the gene core function or downstream phenotype; this term should not be treated as a direct/core annotation. Supporting Evidence: PMID:30916346 GTPBP3 is a highly conserved tRNA modifying enzyme for the biosynthesis of Οm5U at the wobble position of mitochondrial tRNA |
| GO:0070154 mitochondrial lysyl-tRNA aminoacylation | IMP PMID:30916346 Deletion of Gtpbp3 in zebrafish revealed the hypertrophic ca... | MARK AS OVER ANNOTATED | Summary: mitochondrial lysyl-tRNA aminoacylation (GO:0070154) likely overstates or misdirects the direct function of gtpbp3. Reason: The evidence is better explained by the gene core function or downstream phenotype; this term should not be treated as a direct/core annotation. Supporting Evidence: PMID:30916346 GTPBP3 is a highly conserved tRNA modifying enzyme for the biosynthesis of Οm5U at the wobble position of mitochondrial tRNA |
| GO:0070155 mitochondrial methionyl-tRNA aminoacylation | IMP PMID:30916346 Deletion of Gtpbp3 in zebrafish revealed the hypertrophic ca... | MARK AS OVER ANNOTATED | Summary: mitochondrial methionyl-tRNA aminoacylation (GO:0070155) likely overstates or misdirects the direct function of gtpbp3. Reason: The evidence is better explained by the gene core function or downstream phenotype; this term should not be treated as a direct/core annotation. Supporting Evidence: PMID:30916346 GTPBP3 is a highly conserved tRNA modifying enzyme for the biosynthesis of Οm5U at the wobble position of mitochondrial tRNA |
| GO:0070183 mitochondrial tryptophanyl-tRNA aminoacylation | IMP PMID:30916346 Deletion of Gtpbp3 in zebrafish revealed the hypertrophic ca... | MARK AS OVER ANNOTATED | Summary: mitochondrial tryptophanyl-tRNA aminoacylation (GO:0070183) likely overstates or misdirects the direct function of gtpbp3. Reason: The evidence is better explained by the gene core function or downstream phenotype; this term should not be treated as a direct/core annotation. Supporting Evidence: PMID:30916346 GTPBP3 is a highly conserved tRNA modifying enzyme for the biosynthesis of Οm5U at the wobble position of mitochondrial tRNA |
| GO:0070184 mitochondrial tyrosyl-tRNA aminoacylation | IMP PMID:30916346 Deletion of Gtpbp3 in zebrafish revealed the hypertrophic ca... | MARK AS OVER ANNOTATED | Summary: mitochondrial tyrosyl-tRNA aminoacylation (GO:0070184) likely overstates or misdirects the direct function of gtpbp3. Reason: The evidence is better explained by the gene core function or downstream phenotype; this term should not be treated as a direct/core annotation. Supporting Evidence: PMID:30916346 GTPBP3 is a highly conserved tRNA modifying enzyme for the biosynthesis of Οm5U at the wobble position of mitochondrial tRNA |
| GO:0070900 mitochondrial tRNA modification | IMP PMID:30916346 Deletion of Gtpbp3 in zebrafish revealed the hypertrophic ca... | ACCEPT | Summary: mitochondrial tRNA modification (GO:0070900) is supported for gtpbp3. Reason: This annotation matches the synthesized core function or a directly supported core location/process for this gene. Supporting Evidence: PMID:30916346 GTPBP3 is a highly conserved tRNA modifying enzyme for the biosynthesis of Οm5U at the wobble position of mitochondrial tRNA file:DANRE/gtpbp3/gtpbp3-deep-research-falcon.md the **phenotype (cardiomyopathy) + aberrant mitochondrial tRNA metabolism** strongly supports conserving the canonical mitochondrial tRNA wobble-modification function for zebrafish Gtpbp3 |
| GO:0005739 mitochondrion | IDA PMID:27184967 The defective expression of gtpbp3 related to tRNA modificat... | ACCEPT | Summary: mitochondrion (GO:0005739) is supported for gtpbp3. Reason: This annotation matches the synthesized core function or a directly supported core location/process for this gene. Supporting Evidence: PMID:27184967 Zebrafish gtpbp3 has three isoforms localized at mitochondria file:DANRE/gtpbp3/gtpbp3-deep-research-falcon.md GTPBP3 is consistently described as **mitochondrial** (including presence of a mitochondrial targeting sequence and its placement in mitochondrial tRNA modification machinery) |
| GO:0048568 embryonic organ development | IMP PMID:27184967 The defective expression of gtpbp3 related to tRNA modificat... | KEEP AS NON CORE | Summary: embryonic organ development (GO:0048568) is retained as supported context for gtpbp3 but is not the primary/core function. Reason: This annotation is broad, inferred, or reflects downstream developmental/physiological context rather than the central molecular role. Supporting Evidence: PMID:27184967 Zebrafish gtpbp3 has three isoforms localized at mitochondria |
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