amgK encodes an ATP-dependent MurNAc/GlcNAc kinase in peptidoglycan recycling and intrinsic fosfomycin resistance.
Definition: Catalysis of the ATP-dependent phosphorylation of N-acetylmuramate or N-acetylglucosamine at the C1 hydroxyl group.
Justification: The reviewed P. putida AmgK entry and PMID:23831760 define a substrate-specific MurNAc/GlcNAc kinase reaction, while GOA can currently represent only broad carbohydrate kinase activity.
Parent term: carbohydrate kinase activity
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0009254 peptidoglycan turnover | IEA GO_REF:0000041 | ACCEPT | Summary: The IEA peptidoglycan turnover row captures AmgK's recycling-pathway role. Reason: UniProt and the experimental paper place AmgK in a peptidoglycan recycling shortcut. Supporting Evidence: file:PSEPK/amgK/amgK-uniprot.txt Is involved in peptidoglycan recycling file:PSEPK/amgK/amgK-goa.tsv GO:0009254 peptidoglycan turnover file:PSEPK/amgK/amgK-deep-research-falcon.md phosphorylates **N-acetylmuramic acid (MurNAc/NAM)** at the **anomeric carbon (C1)** to produce **MurNAc-Ξ±-1-phosphate (MurNAc-1P)**, a committed intermediate of a **MurU-dependent anabolic peptidoglycan (PG) recycling pathway** that regenerates **UDP-MurNAc** for cell wall synthesis. |
| GO:0005524 ATP binding | IDA PMID:23831760 A cell wall recycling shortcut that bypasses peptidoglycan d... | KEEP AS NON CORE | Summary: ATP binding is necessary for the kinase reaction but is not the informative molecular function. Reason: The core annotation should be kinase activity on MurNAc/GlcNAc substrates. Supporting Evidence: file:PSEPK/amgK/amgK-uniprot.txt ATP-dependent phosphorylation file:PSEPK/amgK/amgK-goa.tsv GO:0005524 ATP binding |
| GO:0009254 peptidoglycan turnover | IMP PMID:23831760 A cell wall recycling shortcut that bypasses peptidoglycan d... | ACCEPT | Summary: The IMP peptidoglycan turnover row is experimentally supported and should be retained. Reason: The AmgK/MurU pathway bypasses de novo UDP-MurNAc synthesis and contributes to peptidoglycan recycling. Supporting Evidence: PMID:23831760 channeling external MurNAc directly to peptidoglycan biosynthesis file:PSEPK/amgK/amgK-goa.tsv GO:0009254 peptidoglycan turnover file:PSEPK/amgK/amgK-deep-research-falcon.md A key organism-specific observation in *P. putida* is that **MurNAc accumulates in a ΞamgK mutant**, consistent with AmgK being required to phosphorylate MurNAc in the salvage route. file:PSEPK/amgK/amgK-deep-research-falcon.md AmgK is positioned after MupP in the anabolic pathway: MupP generates MurNAc from MurNAc-6P, and **AmgK then converts MurNAc into MurNAc-1P** for MurU to form UDP-MurNAc. |
| GO:0019200 carbohydrate kinase activity | IDA PMID:23831760 A cell wall recycling shortcut that bypasses peptidoglycan d... | ACCEPT | Summary: Carbohydrate kinase activity is the best available GO parent for AmgK. Reason: AmgK specifically phosphorylates N-acetylmuramate and N-acetylglucosamine at C1. GO:0019200 correctly captures this reaction class, while the missing substrate-specific term is requested below. Supporting Evidence: file:PSEPK/amgK/amgK-uniprot.txt phosphorylation of N-acetylmuramate (MurNAc) and N-acetylglucosamine file:PSEPK/amgK/amgK-goa.tsv GO:0019200 carbohydrate kinase activity file:PSEPK/amgK/amgK-deep-research-falcon.md AmgK is also described as an **anomeric MurNAc/GlcNAc kinase**, and experimental workflows use AmgK to generate **C1-phosphorylated sugars** from MurNAc and GlcNAc substrates. |
| GO:0097172 N-acetylmuramic acid metabolic process | IDA PMID:23831760 A cell wall recycling shortcut that bypasses peptidoglycan d... | ACCEPT | Summary: N-acetylmuramic acid metabolism is directly supported by AmgK's MurNAc phosphorylation reaction. Reason: The enzyme phosphorylates MurNAc to MurNAc alpha-1-phosphate in the cell-wall recycling pathway. Supporting Evidence: file:PSEPK/amgK/amgK-uniprot.txt leading to MurNAc alpha-1P file:PSEPK/amgK/amgK-goa.tsv GO:0097172 N-acetylmuramic acid metabolic process file:PSEPK/amgK/amgK-deep-research-falcon.md phosphorylates **N-acetylmuramic acid (MurNAc/NAM)** at the **anomeric carbon (C1)** to produce **MurNAc-Ξ±-1-phosphate (MurNAc-1P)**, a committed intermediate of a **MurU-dependent anabolic peptidoglycan (PG) recycling pathway** that regenerates **UDP-MurNAc** for cell wall synthesis. |
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Experiment: Compare sugar-phosphate metabolite levels and fosfomycin sensitivity in wild-type, amgK knockout, and catalytic-site rescue strains.
Type: metabolomics and antibiotic sensitivity assay
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