NAGK (At3g57560) is a chloroplast-stromal N-acetylglutamate kinase that phosphorylates N-acetylglutamate with ATP in Arabidopsis arginine biosynthesis. Its hexameric enzyme is inhibited by arginine; binding of the PII signal protein GLB1 relieves that inhibition under appropriate metabolite conditions. NAGK-dependent arginine supply supports gametophyte function and embryo development. A proteomic study also detects a membrane-associated pool, without establishing a separate cytosolic biosynthetic route.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003991 acetylglutamate kinase activity | IBA GO_REF:0000033 | ACCEPT | Summary: The enzyme-specific activity is supported independently by curated reaction chemistry and target-specific experiments. Reason: The enzyme-specific activity is supported independently by curated reaction chemistry and target-specific experiments. Native biochemical analysis establishes NAG phosphorylation (PMID:16377628), corroborated by complementation of E. coli NAGK deficiency (PMID:28294536). Supporting Evidence: file:ARATH/NAGK/NAGK-uniprot.txt Reaction=N-acetyl-L-glutamate + ATP = N-acetyl-L-glutamyl 5-phosphate + ADP; Xref=Rhea:RHEA:14629, ChEBI:CHEBI:30616, ChEBI:CHEBI:44337, ChEBI:CHEBI:57936, ChEBI:CHEBI:456216; EC=2.7.2.8; Evidence={ECO:0000269|PubMed:16377628}; PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:14630; Evidence={ECO:0000269|PubMed:16377628}; PMID:16377628 The major PII-interacting protein is the chloroplast-localized enzyme N-acetyl glutamate kinase |
| GO:0003991 acetylglutamate kinase activity | IDA PMID:16377628 The PII signal transduction protein of Arabidopsis thaliana ... | ACCEPT | Summary: The enzyme-specific activity is supported independently by curated reaction chemistry and target-specific experiments. Reason: The enzyme-specific activity is supported independently by curated reaction chemistry and target-specific experiments. Native biochemical analysis establishes NAG phosphorylation (PMID:16377628), corroborated by complementation of E. coli NAGK deficiency (PMID:28294536). Supporting Evidence: file:ARATH/NAGK/NAGK-uniprot.txt Reaction=N-acetyl-L-glutamate + ATP = N-acetyl-L-glutamyl 5-phosphate + ADP; Xref=Rhea:RHEA:14629, ChEBI:CHEBI:30616, ChEBI:CHEBI:44337, ChEBI:CHEBI:57936, ChEBI:CHEBI:456216; EC=2.7.2.8; Evidence={ECO:0000269|PubMed:16377628}; PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:14630; Evidence={ECO:0000269|PubMed:16377628}; PMID:16377628 The major PII-interacting protein is the chloroplast-localized enzyme N-acetyl glutamate kinase |
| GO:0003991 acetylglutamate kinase activity | IEA GO_REF:0000120 | ACCEPT | Summary: The enzyme-specific activity is supported independently by curated reaction chemistry and target-specific experiments. Reason: The enzyme-specific activity is supported independently by curated reaction chemistry and target-specific experiments. Native biochemical analysis establishes NAG phosphorylation (PMID:16377628), corroborated by complementation of E. coli NAGK deficiency (PMID:28294536). Supporting Evidence: file:ARATH/NAGK/NAGK-uniprot.txt Reaction=N-acetyl-L-glutamate + ATP = N-acetyl-L-glutamyl 5-phosphate + ADP; Xref=Rhea:RHEA:14629, ChEBI:CHEBI:30616, ChEBI:CHEBI:44337, ChEBI:CHEBI:57936, ChEBI:CHEBI:456216; EC=2.7.2.8; Evidence={ECO:0000269|PubMed:16377628}; PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:14630; Evidence={ECO:0000269|PubMed:16377628}; PMID:16377628 The major PII-interacting protein is the chloroplast-localized enzyme N-acetyl glutamate kinase |
| GO:0005515 protein binding | IPI PMID:15150219 Interactions between the nitrogen signal transduction protei... | REMOVE | Summary: NAGK physically associates with its PII regulator GLB1, with structural and kinetic support. Reason: NAGK physically associates with its PII regulator GLB1, with structural and kinetic support. That regulation remains in the description and core-function evidence. Bare protein binding is removed as uninformative under project policy; no kinase-regulator activity is assigned to NAGK merely because PII regulates it. The ACCase-focused PMID:20018655 also actually identifies NAGK as a positive control, so the removal is not based on its title. Supporting Evidence: file:ARATH/NAGK/NAGK-uniprot.txt Interacts with GLB1. Interaction is dependent of MgATP and inhibited by 2-oxoglutarate, arginine, glutamate, citrate, and oxaloacetate. {ECO:0000269|PubMed:16377628, ECO:0000269|PubMed:17913711, ECO:0000269|PubMed:19631611}. |
| GO:0005515 protein binding | IPI PMID:16377628 The PII signal transduction protein of Arabidopsis thaliana ... | REMOVE | Summary: NAGK physically associates with its PII regulator GLB1, with structural and kinetic support. Reason: NAGK physically associates with its PII regulator GLB1, with structural and kinetic support. That regulation remains in the description and core-function evidence. Bare protein binding is removed as uninformative under project policy; no kinase-regulator activity is assigned to NAGK merely because PII regulates it. The ACCase-focused PMID:20018655 also actually identifies NAGK as a positive control, so the removal is not based on its title. Supporting Evidence: file:ARATH/NAGK/NAGK-uniprot.txt Interacts with GLB1. Interaction is dependent of MgATP and inhibited by 2-oxoglutarate, arginine, glutamate, citrate, and oxaloacetate. {ECO:0000269|PubMed:16377628, ECO:0000269|PubMed:17913711, ECO:0000269|PubMed:19631611}. |
| GO:0005515 protein binding | IPI PMID:17913711 Structural basis for the regulation of N-acetylglutamate kin... | REMOVE | Summary: NAGK physically associates with its PII regulator GLB1, with structural and kinetic support. Reason: NAGK physically associates with its PII regulator GLB1, with structural and kinetic support. That regulation remains in the description and core-function evidence. Bare protein binding is removed as uninformative under project policy; no kinase-regulator activity is assigned to NAGK merely because PII regulates it. The ACCase-focused PMID:20018655 also actually identifies NAGK as a positive control, so the removal is not based on its title. Supporting Evidence: file:ARATH/NAGK/NAGK-uniprot.txt Interacts with GLB1. Interaction is dependent of MgATP and inhibited by 2-oxoglutarate, arginine, glutamate, citrate, and oxaloacetate. {ECO:0000269|PubMed:16377628, ECO:0000269|PubMed:17913711, ECO:0000269|PubMed:19631611}. |
| GO:0005515 protein binding | IPI PMID:19631611 Metabolite regulation of the interaction between Arabidopsis... | REMOVE | Summary: NAGK physically associates with its PII regulator GLB1, with structural and kinetic support. Reason: NAGK physically associates with its PII regulator GLB1, with structural and kinetic support. That regulation remains in the description and core-function evidence. Bare protein binding is removed as uninformative under project policy; no kinase-regulator activity is assigned to NAGK merely because PII regulates it. The ACCase-focused PMID:20018655 also actually identifies NAGK as a positive control, so the removal is not based on its title. Supporting Evidence: file:ARATH/NAGK/NAGK-uniprot.txt Interacts with GLB1. Interaction is dependent of MgATP and inhibited by 2-oxoglutarate, arginine, glutamate, citrate, and oxaloacetate. {ECO:0000269|PubMed:16377628, ECO:0000269|PubMed:17913711, ECO:0000269|PubMed:19631611}. |
| GO:0005515 protein binding | IPI PMID:20018655 Chloroplast acetyl-CoA carboxylase activity is 2-oxoglutarat... | REMOVE | Summary: NAGK physically associates with its PII regulator GLB1, with structural and kinetic support. Reason: NAGK physically associates with its PII regulator GLB1, with structural and kinetic support. That regulation remains in the description and core-function evidence. Bare protein binding is removed as uninformative under project policy; no kinase-regulator activity is assigned to NAGK merely because PII regulates it. The ACCase-focused PMID:20018655 also actually identifies NAGK as a positive control, so the removal is not based on its title. Supporting Evidence: file:ARATH/NAGK/NAGK-uniprot.txt Interacts with GLB1. Interaction is dependent of MgATP and inhibited by 2-oxoglutarate, arginine, glutamate, citrate, and oxaloacetate. {ECO:0000269|PubMed:16377628, ECO:0000269|PubMed:17913711, ECO:0000269|PubMed:19631611}. |
| GO:0005524 ATP binding | IEA GO_REF:0000002 | ACCEPT | Summary: ATP is the phosphate-donor substrate of NAGK and is observed in the NAGK-PII structural study, supporting direct ATP binding rather than a signaling inference from its partner. Reason: ATP is the phosphate-donor substrate of NAGK and is observed in the NAGK-PII structural study, supporting direct ATP binding rather than a signaling inference from its partner. Supporting Evidence: file:ARATH/NAGK/NAGK-uniprot.txt Reaction=N-acetyl-L-glutamate + ATP = N-acetyl-L-glutamyl 5-phosphate + ADP; Xref=Rhea:RHEA:14629, ChEBI:CHEBI:30616, ChEBI:CHEBI:44337, ChEBI:CHEBI:57936, ChEBI:CHEBI:456216; EC=2.7.2.8; Evidence={ECO:0000269|PubMed:16377628}; PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:14630; Evidence={ECO:0000269|PubMed:16377628}; PMID:16377628 The major PII-interacting protein is the chloroplast-localized enzyme N-acetyl glutamate kinase PMID:17913711 bound to the metabolites N-acetylglutamate, ADP, ATP, and arginine. |
| GO:0005737 cytoplasm | IEA GO_REF:0000002 | MODIFY | Summary: Cytoplasm is a broad compartment that includes the chloroplast. Reason: Cytoplasm is a broad compartment that includes the chloroplast. Refine to chloroplast stroma, supported by the native PII-NAGK work and curated localization, without inferring cytosolic arginine synthesis. Proposed replacements: chloroplast stroma Supporting Evidence: file:ARATH/NAGK/NAGK-uniprot.txt Plastid, chloroplast stroma {ECO:0000269|PubMed:16377628}. |
| GO:0005829 cytosol | HDA PMID:28887381 Global Analysis of Membrane-associated Protein Oligomerizati... | MARK AS OVER ANNOTATED | Summary: The native biochemical localization is chloroplast stroma, and the cited fractionation study itself classifies NAGK as a plastid protein, so the cytosol assignment over-states the data. Reason: PMID:28887381 is a protein-correlation-profiling study of soluble and microsomal fractions from whole leaves, an assay that cannot resolve whether a soluble protein came from cytosol or from broken plastids. In the paper's own supplement, NAGK is classified as plastid and membrane-associated, with no dual-localization flag, so the paper does not itself assign NAGK to cytosol. Direct biochemical localization places NAGK in the chloroplast stroma (PMID:16377628, curated in UniProt). An additional small cytosolic pool is not excluded, so the row is marked as an over-annotation rather than removed. Supporting Evidence: file:ARATH/NAGK/NAGK-source-analysis/README.md Subacon localization is plastid, True membrane is True, and Dual Localized is empty. file:ARATH/NAGK/NAGK-uniprot.txt Plastid, chloroplast stroma {ECO:0000269|PubMed:16377628}. |
| GO:0006526 L-arginine biosynthetic process | IBA GO_REF:0000033 | ACCEPT | Summary: The protein directly catalyzes an acetylated-intermediate reaction that produces an arginine/ornithine precursor, so it participates in the biosynthetic process. Reason: The protein directly catalyzes an acetylated-intermediate reaction that produces an arginine/ornithine precursor, so it participates in the biosynthetic process. Target-specific functional evidence supports the enzymatic role rather than reliance on knockout necessity alone. Supporting Evidence: file:ARATH/NAGK/NAGK-uniprot.txt Reaction=N-acetyl-L-glutamate + ATP = N-acetyl-L-glutamyl 5-phosphate + ADP; Xref=Rhea:RHEA:14629, ChEBI:CHEBI:30616, ChEBI:CHEBI:44337, ChEBI:CHEBI:57936, ChEBI:CHEBI:456216; EC=2.7.2.8; Evidence={ECO:0000269|PubMed:16377628}; PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:14630; Evidence={ECO:0000269|PubMed:16377628}; PMID:16377628 The major PII-interacting protein is the chloroplast-localized enzyme N-acetyl glutamate kinase file:ARATH/NAGK/NAGK-uniprot.txt Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-acetyl- L-ornithine from L-glutamate: step 2/4. {ECO:0000305|PubMed:17913711}. |
| GO:0006526 L-arginine biosynthetic process | IEA GO_REF:0000120 | ACCEPT | Summary: The protein directly catalyzes an acetylated-intermediate reaction that produces an arginine/ornithine precursor, so it participates in the biosynthetic process. Reason: The protein directly catalyzes an acetylated-intermediate reaction that produces an arginine/ornithine precursor, so it participates in the biosynthetic process. Target-specific functional evidence supports the enzymatic role rather than reliance on knockout necessity alone. Supporting Evidence: file:ARATH/NAGK/NAGK-uniprot.txt Reaction=N-acetyl-L-glutamate + ATP = N-acetyl-L-glutamyl 5-phosphate + ADP; Xref=Rhea:RHEA:14629, ChEBI:CHEBI:30616, ChEBI:CHEBI:44337, ChEBI:CHEBI:57936, ChEBI:CHEBI:456216; EC=2.7.2.8; Evidence={ECO:0000269|PubMed:16377628}; PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:14630; Evidence={ECO:0000269|PubMed:16377628}; PMID:16377628 The major PII-interacting protein is the chloroplast-localized enzyme N-acetyl glutamate kinase file:ARATH/NAGK/NAGK-uniprot.txt Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-acetyl- L-ornithine from L-glutamate: step 2/4. {ECO:0000305|PubMed:17913711}. |
| GO:0006526 L-arginine biosynthetic process | TAS PMID:16377628 The PII signal transduction protein of Arabidopsis thaliana ... | ACCEPT | Summary: The protein directly catalyzes an acetylated-intermediate reaction that produces an arginine/ornithine precursor, so it participates in the biosynthetic process. Reason: The protein directly catalyzes an acetylated-intermediate reaction that produces an arginine/ornithine precursor, so it participates in the biosynthetic process. Target-specific functional evidence supports the enzymatic role rather than reliance on knockout necessity alone. Supporting Evidence: file:ARATH/NAGK/NAGK-uniprot.txt Reaction=N-acetyl-L-glutamate + ATP = N-acetyl-L-glutamyl 5-phosphate + ADP; Xref=Rhea:RHEA:14629, ChEBI:CHEBI:30616, ChEBI:CHEBI:44337, ChEBI:CHEBI:57936, ChEBI:CHEBI:456216; EC=2.7.2.8; Evidence={ECO:0000269|PubMed:16377628}; PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:14630; Evidence={ECO:0000269|PubMed:16377628}; PMID:16377628 The major PII-interacting protein is the chloroplast-localized enzyme N-acetyl glutamate kinase file:ARATH/NAGK/NAGK-uniprot.txt Amino-acid biosynthesis; L-arginine biosynthesis; N(2)-acetyl- L-ornithine from L-glutamate: step 2/4. {ECO:0000305|PubMed:17913711}. |
| GO:0009507 chloroplast | HDA PMID:18431481 Sorting signals, N-terminal modifications and abundance of t... | MODIFY | Summary: Chloroplast localization is independently supported. Reason: Chloroplast localization is independently supported. Refine to the stromal compartment already represented in this review, using the native chloroplast PII-NAGK biochemical study (PMID:16377628). Proposed replacements: chloroplast stroma Supporting Evidence: file:ARATH/NAGK/NAGK-uniprot.txt Plastid, chloroplast stroma {ECO:0000269|PubMed:16377628}. |
| GO:0009507 chloroplast | IDA PMID:16377628 The PII signal transduction protein of Arabidopsis thaliana ... | MODIFY | Summary: Chloroplast localization is independently supported. Reason: Chloroplast localization is independently supported. Refine to the stromal compartment already represented in this review, using the native chloroplast PII-NAGK biochemical study (PMID:16377628). Proposed replacements: chloroplast stroma Supporting Evidence: file:ARATH/NAGK/NAGK-uniprot.txt Plastid, chloroplast stroma {ECO:0000269|PubMed:16377628}. |
| GO:0009507 chloroplast | ISM GO_REF:0000122 | MODIFY | Summary: Chloroplast localization is independently supported. Reason: Chloroplast localization is independently supported. Refine to the stromal compartment already represented in this review, using the native chloroplast PII-NAGK biochemical study (PMID:16377628). Proposed replacements: chloroplast stroma Supporting Evidence: file:ARATH/NAGK/NAGK-uniprot.txt Plastid, chloroplast stroma {ECO:0000269|PubMed:16377628}. |
| GO:0009534 chloroplast thylakoid | HDA PMID:20061580 AT_CHLORO, a comprehensive chloroplast proteome database wit... | KEEP AS NON CORE | Summary: AT_CHLORO subfraction proteomics assigns a NAGK pool to thylakoids; an independent study also detects a membrane-associated NAGK pool, so the curated HDA row is retained as a non-core location. Reason: AT_CHLORO (PMID:20061580) assigned subplastidial localization by spectral counting across stroma, thylakoid and envelope fractions of purified chloroplasts. The NAGK-specific counts are in the database rather than the cached text, so the TAIR curator's experimental call is deferred to rather than overruled. That call is consistent with independent evidence for a membrane-associated plastid NAGK pool in PMID:28887381. The catalytic and PII-regulated function of NAGK is stromal (PMID:16377628), so thylakoid association is kept as non-core and not used as the site of the core activity. Supporting Evidence: PMID:20061580 We assessed the partitioning of each protein in the three chloroplast compartments by using a semiquantitative proteomics approach (spectral count). file:ARATH/NAGK/NAGK-source-analysis/README.md These data support a membrane-associated pool but do not independently identify a cytosolic compartment or a particular chloroplast membrane. |
| GO:0009570 chloroplast stroma | IEA GO_REF:0000044 | ACCEPT | Summary: Retain the stromal localization of this soluble chloroplast amino-acid-biosynthetic enzyme. Reason: Retain the stromal localization of this soluble chloroplast amino-acid-biosynthetic enzyme. The native PII-NAGK study and curated experimental localization directly support stroma. Supporting Evidence: file:ARATH/NAGK/NAGK-uniprot.txt Plastid, chloroplast stroma {ECO:0000269|PubMed:16377628}. |
| GO:0016301 kinase activity | IEA GO_REF:0000002 | MODIFY | Summary: The generic catalytic class is true but the specific substrate reaction is established independently and already represented here. Reason: The generic catalytic class is true but the specific substrate reaction is established independently and already represented here. Refine the term to the demonstrated biosynthetic enzyme activity. Proposed replacements: acetylglutamate kinase activity Supporting Evidence: file:ARATH/NAGK/NAGK-uniprot.txt Reaction=N-acetyl-L-glutamate + ATP = N-acetyl-L-glutamyl 5-phosphate + ADP; Xref=Rhea:RHEA:14629, ChEBI:CHEBI:30616, ChEBI:CHEBI:44337, ChEBI:CHEBI:57936, ChEBI:CHEBI:456216; EC=2.7.2.8; Evidence={ECO:0000269|PubMed:16377628}; PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:14630; Evidence={ECO:0000269|PubMed:16377628}; PMID:16377628 The major PII-interacting protein is the chloroplast-localized enzyme N-acetyl glutamate kinase |
| GO:0034618 arginine binding | IDA PMID:17913711 Structural basis for the regulation of N-acetylglutamate kin... | ACCEPT | Summary: Arginine binds the regulatory sites of NAGK and inhibits catalysis. Reason: Arginine binds the regulatory sites of NAGK and inhibits catalysis. The native complex structure contains arginine, and kinetic studies show relief of feedback inhibition by PII; binding is a direct regulatory property of NAGK. Supporting Evidence: file:ARATH/NAGK/NAGK-uniprot.txt Inhibited by arginine. Inhibition is relieved by binding to GLB1. {ECO:0000269|PubMed:16377628, ECO:0000269|PubMed:19631611}. PMID:17913711 a domain-separating inhibitory effect exerted by arginine |
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