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 | ACCEPT | Summary: Alanyl-tRNA aminoacylation is the core biological process for this enzyme. Reason: The enzyme charges tRNA(Ala) with alanine, directly performing this process for organellar protein translation. Supporting Evidence: file:POPTR/ALARS/ALARS-uniprot.txt Catalyzes the attachment of alanine to tRNA(Ala) file:POPTR/ALARS/ALARS-uniprot.txt DR GO; GO:0006419; P:alanyl-tRNA aminoacylation; IBA:GO_Central. |
| 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 file:POPTR/ALARS/ALARS-uniprot.txt DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule. |
| 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 | ACCEPT | Summary: Duplicate IEA annotation of the core alanyl-tRNA aminoacylation process, consistent with the IBA annotation. Reason: The enzyme charges tRNA(Ala) with alanine for organellar translation. Supporting Evidence: file:POPTR/ALARS/ALARS-uniprot.txt Catalyzes the attachment of alanine to tRNA(Ala) file:POPTR/ALARS/ALARS-uniprot.txt DR GO; GO:0006419; P:alanyl-tRNA aminoacylation; IBA:GO_Central. |
| 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 | KEEP AS NON CORE | Summary: tRNA aminoacylation is correct but is the generic parent of the specific alanyl-tRNA aminoacylation process also annotated. Reason: The specific alanyl-tRNA aminoacylation term (GO:0006419) better captures the process than this broad parent, which is true but redundant and so is retained as a non-core annotation. Supporting Evidence: file:POPTR/ALARS/ALARS-uniprot.txt Catalyzes the attachment of alanine to tRNA(Ala) file:POPTR/ALARS/ALARS-uniprot.txt DR GO; GO:0006419; P:alanyl-tRNA aminoacylation; IBA:GO_Central. |
| 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
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