Organellar alanyl-tRNA synthetase (alanine--tRNA ligase) that catalyzes the ATP-dependent attachment of L-alanine to tRNA(Ala), generating the L-alanyl-tRNA(Ala) substrate for protein translation. The reaction proceeds in two steps: alanine is first activated by ATP to form Ala-AMP, then transferred to the acceptor end of tRNA(Ala). The enzyme also has a proofreading/editing (deacylase) activity that removes incorrectly charged amino acids from mischarged tRNA(Ala), ensuring translational fidelity. It is a class-II aminoacyl-tRNA synthetase that binds one zinc ion per subunit and consists of an N-terminal catalytic domain, an editing domain, and a C-terminal C-Ala domain. The protein is dual-targeted to the chloroplast and mitochondrion via an N-terminal transit peptide.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004813 alanine-tRNA ligase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Alanine-tRNA ligase activity is the core molecular function of this enzyme. Reason: UniProt curates the aminoacylation reaction and EC 6.1.1.7 for this protein. Supporting Evidence: file:POPTR/ALARS/ALARS-uniprot.txt Catalyzes the attachment of alanine to tRNA(Ala) file:POPTR/ALARS/ALARS-uniprot.txt Reaction=tRNA(Ala) + L-alanine + ATP = L-alanyl-tRNA(Ala) + AMP + |
| GO:0002161 aminoacyl-tRNA deacylase activity | IBA GO_REF:0000033 | ACCEPT | Summary: Aminoacyl-tRNA deacylase (editing/proofreading) activity is a genuine secondary molecular function via the dedicated editing domain. Reason: UniProt describes an editing domain that removes incorrectly charged amino acids and stimulates deacylation of misacylated tRNAs. Supporting Evidence: file:POPTR/ALARS/ALARS-uniprot.txt Also edits incorrectly charged tRNA(Ala) via its editing domain. file:POPTR/ALARS/ALARS-uniprot.txt The editing domain removes incorrectly charged amino acids |
| GO:0005829 cytosol | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: Cytosol localization conflicts with the curated organellar (chloroplast and mitochondrion) targeting of this dual-targeted plant AlaRS and likely reflects the cytoplasmic AlaRS phylogenetic neighbors. Reason: UniProt curates plastid/chloroplast and mitochondrion localization with an N-terminal organellar transit peptide; the cytosol annotation is transferred from cytoplasmic AlaRS orthologs and is not supported for this protein. Propagation Review Root cause: PROPAGATION BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH Sources checked: PANTHER:PTN000207063 SUPPORTS SOURCE BUT NOT TARGET IBD node covers cytoplasmic AlaRS members; the poplar protein carries an organellar transit peptide and is plastid/mitochondrial, so the cytosol component should not transfer. UniProtKB:P00957 · E. coli alanine--tRNA ligase AlaS SUPPORTS SOURCE BUT NOT TARGET Supporting Evidence: file:POPTR/ALARS/ALARS-uniprot.txt SUBCELLULAR LOCATION: Plastid, chloroplast file:POPTR/ALARS/ALARS-uniprot.txt /note="Chloroplast and mitochondrion" |
| GO:0006419 alanyl-tRNA aminoacylation | IBA GO_REF:0000033 | MODIFY | Summary: Retain the supported biology under the current process term; the source GO identifier is obsolete. Reason: GO explicitly replaces obsolete GO:0006419 with GO:0006418. Alanine specificity remains in GO:0004813 and the supported reaction; this migration does not question the original experimental or phylogenetic evidence. The enzyme charges tRNA(Ala) with alanine, directly performing this process for organellar protein translation. Proposed replacements: tRNA aminoacylation for protein translation Supporting Evidence: file:POPTR/ALARS/ALARS-uniprot.txt Catalyzes the attachment of alanine to tRNA(Ala) |
| GO:0000166 nucleotide binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Nucleotide binding is correct but is a generic parent of the more specific ATP binding activity that is also annotated. Reason: The enzyme binds ATP during the activation step; the generic nucleotide binding term is true but less informative than the ATP binding annotation also present, so it is retained as a non-core annotation. Supporting Evidence: file:POPTR/ALARS/ALARS-uniprot.txt alanine is first activated by ATP to form Ala-AMP file:POPTR/ALARS/ALARS-uniprot.txt DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule. |
| GO:0003676 nucleic acid binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Nucleic acid binding is correct (the enzyme binds tRNA(Ala)) but is an overly generic parent of the specific tRNA binding annotated by UniProt. Reason: The functionally meaningful binding is tRNA(Ala) binding; the broad nucleic acid binding parent is true but uninformative for this aminoacyl-tRNA synthetase, so it is retained as a non-core annotation. Supporting Evidence: file:POPTR/ALARS/ALARS-uniprot.txt DR GO; GO:0000049; F:tRNA binding; IEA:UniProtKB-KW. file:POPTR/ALARS/ALARS-uniprot.txt Catalyzes the attachment of alanine to tRNA(Ala) |
| GO:0004812 aminoacyl-tRNA ligase activity | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Aminoacyl-tRNA ligase activity is correct but is the generic parent of the specific alanine-tRNA ligase activity that is also annotated. Reason: The specific alanine-tRNA ligase activity (GO:0004813) better captures the curated catalytic activity than this family-level parent term, which is true but redundant and so is retained as a non-core annotation. Supporting Evidence: file:POPTR/ALARS/ALARS-uniprot.txt Reaction=tRNA(Ala) + L-alanine + ATP = L-alanyl-tRNA(Ala) + AMP + file:POPTR/ALARS/ALARS-uniprot.txt DR GO; GO:0004813; F:alanine-tRNA ligase activity; IBA:GO_Central. |
| GO:0004813 alanine-tRNA ligase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Duplicate IEA annotation of the core alanine-tRNA ligase activity, consistent with the IBA annotation. Reason: UniProt curates EC 6.1.1.7 and the aminoacylation reaction for this protein. Supporting Evidence: file:POPTR/ALARS/ALARS-uniprot.txt Reaction=tRNA(Ala) + L-alanine + ATP = L-alanyl-tRNA(Ala) + AMP + file:POPTR/ALARS/ALARS-uniprot.txt EC=6.1.1.7 |
| GO:0005524 ATP binding | IEA GO_REF:0000120 | ACCEPT | Summary: ATP binding is supported; ATP is required to activate alanine in the first step of aminoacylation. Reason: The catalytic reaction consumes ATP to form the Ala-AMP intermediate. Supporting Evidence: file:POPTR/ALARS/ALARS-uniprot.txt alanine is first activated by ATP to form Ala-AMP |
| GO:0005737 cytoplasm | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: Cytoplasm is a broad parent term that encompasses the curated chloroplast and mitochondrion localizations of this dual-targeted AlaRS but is less informative than them. Reason: In GO the plastid and mitochondrion are part of the cytoplasm, so this broad term is technically correct but redundant with the specific organellar locations; it is retained as a non-core annotation rather than the principal localization. Supporting Evidence: file:POPTR/ALARS/ALARS-uniprot.txt SUBCELLULAR LOCATION: Plastid, chloroplast file:POPTR/ALARS/ALARS-uniprot.txt /note="Chloroplast and mitochondrion" |
| GO:0005739 mitochondrion | IEA GO_REF:0000120 | ACCEPT | Summary: Mitochondrion localization is supported by the curated subcellular location and dual organellar targeting. Reason: UniProt curates mitochondrion as a subcellular location for this dual-targeted enzyme. Supporting Evidence: file:POPTR/ALARS/ALARS-uniprot.txt Mitochondrion {ECO:0000255|HAMAP-Rule:MF_03134}. file:POPTR/ALARS/ALARS-uniprot.txt DR GO; GO:0005739; C:mitochondrion; IEA:UniProtKB-SubCell. |
| GO:0006419 alanyl-tRNA aminoacylation | IEA GO_REF:0000120 | MODIFY | Summary: Retain the supported biology under the current process term; the source GO identifier is obsolete. Reason: GO explicitly replaces obsolete GO:0006419 with GO:0006418. Alanine specificity remains in GO:0004813 and the supported reaction; this migration does not question the original experimental or phylogenetic evidence. The enzyme charges tRNA(Ala) with alanine for organellar translation. Proposed replacements: tRNA aminoacylation for protein translation Supporting Evidence: file:POPTR/ALARS/ALARS-uniprot.txt Catalyzes the attachment of alanine to tRNA(Ala) |
| GO:0008270 zinc ion binding | IEA GO_REF:0000104 | ACCEPT | Summary: Zinc ion binding is supported; the enzyme binds one zinc ion per subunit via defined coordinating residues. Reason: UniProt curates a Zn(2+) cofactor with explicit binding residues. Supporting Evidence: file:POPTR/ALARS/ALARS-uniprot.txt Note=Binds 1 zinc ion per subunit. file:POPTR/ALARS/ALARS-uniprot.txt DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule. |
| GO:0009507 chloroplast | IEA GO_REF:0000120 | ACCEPT | Summary: Chloroplast localization is supported by the curated plastid subcellular location and dual organellar targeting. Reason: UniProt curates plastid/chloroplast as a subcellular location for this enzyme. Supporting Evidence: file:POPTR/ALARS/ALARS-uniprot.txt SUBCELLULAR LOCATION: Plastid, chloroplast file:POPTR/ALARS/ALARS-uniprot.txt DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell. |
| GO:0043039 tRNA aminoacylation | IEA GO_REF:0000002 | MODIFY | Summary: ALARS charges tRNA for organellar protein translation. Reason: Refine generic tRNA aminoacylation to the supported translational charging process GO:0006418. Alanine specificity is represented by GO:0004813; the former process GO:0006419 is obsolete. Proposed replacements: tRNA aminoacylation for protein translation Supporting Evidence: file:POPTR/ALARS/ALARS-uniprot.txt Catalyzes the attachment of alanine to tRNA(Ala) |
| GO:0106074 aminoacyl-tRNA metabolism involved in translational fidelity | IEA GO_REF:0000108 | ACCEPT | Summary: This term correctly captures the proofreading/editing role of the enzyme in maintaining translational fidelity. Reason: The editing domain removes mischarged amino acids and stimulates deacylation of misacylated tRNAs, supporting translational fidelity. Supporting Evidence: file:POPTR/ALARS/ALARS-uniprot.txt Also edits incorrectly charged tRNA(Ala) via its editing domain. file:POPTR/ALARS/ALARS-uniprot.txt stimulating deacylation of misacylated tRNAs. |
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Download this section (compressed HTML)Q: Is the dual chloroplast/mitochondrion targeting of poplar AlaRS achieved through alternative transcription/translation start sites or a single ambiguous transit peptide?
Experiment: Express the N-terminal transit peptide fused to a fluorescent reporter and assess chloroplast versus mitochondrion targeting in poplar protoplasts, and assay recombinant enzyme for aminoacylation and editing (deacylation of Ser/Gly-tRNA-Ala) activities.
Type: subcellular targeting and enzyme biochemistry
Migrated the authored core process from GO:0006419 to GO:0006418, and reconciled affected annotation decisions and proposed replacements. Original GOA identifiers, labels, evidence and row counts remain unchanged. The underlying reaction and supported molecular function are retained. Term status and migration metadata are documented in modules/bacterial_aminoacyl_trna_charging-analysis/ontology-review.md and the pinned GO source stanzas.
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