amgK

UniProt ID: Q88QT3
Organism: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
Review Status: DRAFT
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Gene Description

amgK encodes an ATP-dependent MurNAc/GlcNAc kinase in peptidoglycan recycling and intrinsic fosfomycin resistance.

Proposed New Ontology Terms

N-acetylmuramate/N-acetylglucosamine kinase activity

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:

Existing Annotations Review

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-α-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 ΔamgK 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... 		MARK AS OVER ANNOTATED
Summary: Carbohydrate kinase activity is correct but too broad for AmgK's substrate-specific activity.
Reason: AmgK specifically phosphorylates N-acetylmuramate and N-acetylglucosamine at C1; GOA lacks a specific MurNAc/GlcNAc kinase term, which is requested below in proposed_new_terms.
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-α-1-phosphate (MurNAc-1P)**, a committed intermediate of a **MurU-dependent anabolic peptidoglycan (PG) recycling pathway** that regenerates **UDP-MurNAc** for cell wall synthesis.

Core Functions

ATP-dependent MurNAc/GlcNAc kinase that channels recycled cell-wall sugars into peptidoglycan precursor metabolism; no exact current GO molecular-function term exists, so the specific activity is requested in proposed_new_terms.

Directly Involved In:
peptidoglycan turnover N-acetylmuramic acid metabolic process
Supporting Evidence:
  • file:PSEPK/amgK/amgK-uniprot.txt
    phosphorylation of N-acetylmuramate (MurNAc) and N-acetylglucosamine
  • PMID:23831760
    anomeric sugar kinase AmgK
  • file:PSEPK/amgK/amgK-deep-research-falcon.md
    phosphorylates **N-acetylmuramic acid (MurNAc/NAM)** at the **anomeric carbon (C1)** to produce **MurNAc-α-1-phosphate (MurNAc-1P)**, a committed intermediate of a **MurU-dependent anabolic peptidoglycan (PG) recycling pathway** that regenerates **UDP-MurNAc** for cell wall synthesis.
  • file:PSEPK/amgK/amgK-deep-research-falcon.md
    This recycling “shortcut” bypasses the canonical **MurA/MurB** de novo pathway and contributes to **intrinsic fosfomycin resistance** in pseudomonads because fosfomycin targets MurA.

References

GO_REF:0000041
Gene Ontology annotation based on UniPathway vocabulary mapping
PMID:23831760
A cell wall recycling shortcut that bypasses peptidoglycan de novo biosynthesis.
file:PSEPK/amgK/amgK-uniprot.txt
UniProtKB reviewed entry for amgK
  • UniProt provides the reviewed functional description used for the amgK review.
file:PSEPK/amgK/amgK-goa.tsv
QuickGO GOA annotations for amgK
  • The fetched GOA table contains the annotations reviewed for amgK.
file:interpro/panther/PTHR33540/PTHR33540-metadata.yaml
PANTHER family metadata for amgK
  • PANTHER places AmgK in the anomeric sugar kinase clade of the TsaE/AmgK kinase family.
file:PSEPK/amgK/amgK-deep-research-falcon.md
Falcon (Edison Scientific) deep research report on amgK (PP_0405; Q88QT3)
  • AmgK phosphorylates MurNAc at the anomeric carbon (C1) to produce MurNAc-alpha-1-phosphate, the committed intermediate of the MurU-dependent anabolic peptidoglycan recycling pathway.
    "phosphorylates **N-acetylmuramic acid (MurNAc/NAM)** at the **anomeric carbon (C1)** to produce **MurNAc-α-1-phosphate (MurNAc-1P)**, a committed intermediate of a **MurU-dependent anabolic peptidoglycan (PG) recycling pathway** that regenerates **UDP-MurNAc** for cell wall synthesis."
  • The recycling pathway bypasses the de novo MurA/MurB route and confers intrinsic fosfomycin resistance, since fosfomycin targets MurA.
    "This recycling “shortcut” bypasses the canonical **MurA/MurB** de novo pathway and contributes to **intrinsic fosfomycin resistance** in pseudomonads because fosfomycin targets MurA."
  • AmgK is an anomeric MurNAc/GlcNAc kinase generating C1-phosphorylated sugars from both MurNAc and GlcNAc.
    "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."
  • MurNAc accumulates in a P. putida amgK deletion mutant, confirming AmgK is required for the MurNAc phosphorylation step of the salvage route.
    "A key organism-specific observation in *P. putida* is that **MurNAc accumulates in a ΔamgK mutant**, consistent with AmgK being required to phosphorylate MurNAc in the salvage route."
  • AmgK acts downstream of MupP in the anabolic recycling route, converting MurNAc to MurNAc-1P for MurU to form UDP-MurNAc.
    "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."
  • AmgK is inferred to act in the cytoplasm, consistent with the cytosolic processing of imported peptidoglycan fragments.
    "This supports the inference that AmgK functions in the **cytoplasm**."

Suggested Questions for Experts

Q: What are the in vivo relative contributions of MurNAc, GlcNAc, and GalNAc phosphorylation by AmgK during KT2440 cell-wall recycling?

Suggested Experiments

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

Deep Research

Falcon

(amgK-deep-research-falcon.md)
Research Report: Functional Annotation of **amgK** (PP_0405; UniProt **Q88QT3**) in *Pseudomonas putida* KT2440 Falcon Edison Scientific Literature 27 citations 1 artifacts 2026-06-01T07:03:53.185129
Edison artifact artifact-00 (text/markdown)

The research report should be a detailed narrative explaining the function, biological processes, and localization of the gene product. Citations should be given for all claims.

You should prioritize authoritative reviews and primary scientific literature when conducting research. You can supplement
this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.

We are specifically interested in the primary function of the gene - for enzymes, what reaction is catalyzed, and what is the substrate specificity? For transporters, what is the substrate? For structural proteins or adapters, what is the broader structural role? For signaling molecules, what is the role in the pathway.

We are interested in where in or outside the cell the gene product carries out its function.

We are also interested in the signaling or biochemical pathways in which the gene functions. We are less interested in broad pleiotropic effects, except where these elucidate the precise role.

Include evidence where possible. We are interested in both experimental evidence as well as inference from structure, evolution, or bioinformatic analysis. Precise studies should be prioritized over high-throughput, where available.

Research Report: Functional Annotation of amgK (PP_0405; UniProt Q88QT3) in Pseudomonas putida KT2440

Executive summary

The Pseudomonas putida KT2440 gene amgK (locus PP_0405, UniProt Q88QT3) encodes an anomeric amino-sugar kinase that phosphorylates N-acetylmuramic acid (MurNAc/NAM) at the anomeric carbon (C1) to produce MurNAc-α-1-phosphate (MurNAc-1P), a committed intermediate of a MurU-dependent anabolic peptidoglycan (PG) recycling pathway that regenerates UDP-MurNAc for cell wall synthesis. This recycling “shortcut” bypasses the canonical MurA/MurB de novo pathway and contributes to intrinsic fosfomycin resistance in pseudomonads because fosfomycin targets MurA. (borisova2017thenacetylmuramic pages 2-4, borisova2017thenacetylmuramic pages 9-11)

Recent (2024) work has leveraged AmgK/MurU-dependent NAM recycling as a real-world implementation for rapid, live-cell peptidoglycan imaging and antibiotic-screening-enabling assays, demonstrating second-scale bioorthogonal labeling kinetics and NAM-probe incorporation in P. putida and P. aeruginosa. (hillman2024minimalisttetrazinenacetyl pages 6-7, hillman2024minimalisttetrazinenacetyl pages 4-6)

Target identity verification (mandatory)

Gene/protein match

Multiple organism-specific sources identify amgK in P. putida KT2440 as PP_0405, discovered adjacent to murU (pp0406) and functioning in the AmgK–MurU anabolic recycling pathway. This matches UniProt Q88QT3’s description as an N-acetylmuramate/N-acetylglucosamine kinase (MurNAc/GlcNAc kinase; “anomeric sugar kinase”) of the AmgK family. (borisova2017thenacetylmuramic pages 2-4)

Avoiding symbol ambiguity

In the retrieved literature, amgK consistently refers to the MurNAc/GlcNAc anomeric kinase in the MurU salvage pathway (not an unrelated enzyme with the same symbol). No conflicting identity for P. putida KT2440 PP_0405 was encountered. (borisova2017thenacetylmuramic pages 2-4, borisova2017thenacetylmuramic pages 9-11)

1) Key concepts and definitions (current understanding)

Peptidoglycan recycling and MurNAc salvage

Peptidoglycan (PG) is turned over during growth, generating fragments that many bacteria import and recycle. In E. coli, MurNAc-derived fragments typically feed a catabolic route requiring MurQ. In contrast, many Gram-negative bacteria including Pseudomonas spp. lack MurQ and instead use an anabolic recycling route that returns MurNAc to the biosynthetic precursor pool (UDP-MurNAc). (borisova2017thenacetylmuramic pages 2-4)

The “MurU pathway” / anabolic PG recycling route

In Pseudomonas, the anabolic route includes:
- AnmK (anhydro-MurNAc kinase) converting anhydro-MurNAc to a phosphorylated MurNAc intermediate,
- a MurNAc-6P phosphatase (MupP) converting MurNAc-6P → MurNAc,
- AmgK converting MurNAc → MurNAc-1P (anomeric phosphorylation),
- MurU converting MurNAc-1P → UDP-MurNAc. (borisova2017thenacetylmuramic pages 2-4, zheng2022differencesinfosfomycin pages 3-4)

This route bypasses de novo UDP-MurNAc synthesis by MurA/MurB, the step inhibited by fosfomycin, explaining a mechanistic link to intrinsic resistance. (borisova2017thenacetylmuramic pages 2-4, zheng2022differencesinfosfomycin pages 3-4)

2) Molecular function of AmgK (reaction, substrate specificity)

Catalyzed reaction

AmgK is described as a sugar kinase in the anabolic pathway that generates MurNAc-1P used by MurU to produce UDP-MurNAc. (borisova2017thenacetylmuramic pages 2-4)

The reaction can be summarized as:
- MurNAc + ATP → MurNAc-α-1-phosphate + ADP

Substrate scope (MurNAc and GlcNAc)

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. (borisova2017thenacetylmuramic pages 2-4)

A 2024 in vitro chemoenzymatic assay using purified proteins reports that AmgK can convert multiple MurNAc-derived probes (“NAM probes”) into the corresponding α-1-phosphate products, indicating substrate permissiveness to modifications on MurNAc in that experimental context. (hillman2024minimalisttetrazinenacetyl pages 4-6)

Enzyme kinetics/structure: current evidence limitations

Within the retrieved full texts, direct kinetic constants or structures for P. putida AmgK were not available. However, the Pseudomonas pathway paper reports that kinetic parameters for “other recycling enzymes (AnmK, AmgK, MurK, and MurQ)” fall in the range Km ≈ 180–1,200 μM and kcat ≈ 5–6 s⁻¹ under conditions spanning 25–37°C, implying AmgK operates with enzyme efficiencies typical of cytosolic sugar-processing enzymes, but without isolating AmgK-specific values in the available excerpt. (borisova2017thenacetylmuramic pages 9-11)

3) Biological process and pathway integration in P. putida KT2440

Genomic context

The pathway paper reports that bioinformatic searches in pseudomonad genomes identified murU (pp0406) and the adjacent gene pp0405 (amgK). (borisova2017thenacetylmuramic pages 2-4)

Functional role in the anabolic recycling route

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. (borisova2017thenacetylmuramic pages 2-4)

Genetic and metabolite evidence (organism-specific)

A key organism-specific observation in P. putida is that MurNAc accumulates in a ΔamgK mutant, consistent with AmgK being required to phosphorylate MurNAc in the salvage route. (borisova2017thenacetylmuramic pages 2-4)

4) Cellular localization

Likely subcellular site of action: cytoplasm

The anabolic recycling pathway is described as a set of enzymatic steps acting on imported and cytosol-processed PG fragments and was experimentally assessed using cytosolic fractions (for pathway intermediates/precursors). This supports the inference that AmgK functions in the cytoplasm. No direct microscopy or fractionation experiment for AmgK itself was retrieved. (borisova2017thenacetylmuramic pages 2-4, borisova2017thenacetylmuramic pages 4-7)

5) Phenotypes and physiological relevance

Fosfomycin resistance linkage

Fosfomycin inhibits MurA, the first committed step of de novo UDP-MurNAc synthesis. In bacteria with the anabolic recycling pathway, fosfomycin is less effective because UDP-MurNAc can be regenerated via MurU salvage. (borisova2017thenacetylmuramic pages 2-4)

Consistent with this mechanism:
- The pathway paper notes up to 8-fold increased fosfomycin susceptibility in P. aeruginosa PG recycling mutants, and indicates prior work showing that deletion of recycling genes including amgK increases fosfomycin susceptibility in P. putida. (borisova2017thenacetylmuramic pages 2-4, zheng2022differencesinfosfomycin pages 4-6)
- A 2022 narrative review summarizes that blocking the salvage pathway yields ~4- to 8-fold increased fosfomycin susceptibility. (zheng2022differencesinfosfomycin pages 3-4)

PG precursor pool effects (pathway-level context)

Although the retrieved quantitative metabolomics were centered on mupP, the same work shows that blocking the anabolic pathway can strongly reduce precursor pools (e.g., UDP-MurNAc), providing a biochemical rationale for fosfomycin hypersensitivity when recycling is blocked. (borisova2017thenacetylmuramic pages 4-7, borisova2017thenacetylmuramic pages 9-11)

Connection to β-lactam resistance via cell-wall recycling (context beyond P. putida)

While not specific to P. putida, high-density transposon mutagenesis in an MDR P. aeruginosa isolate identified the entire salvage pathway (AnmK/AmgK/MupP/MurU) as part of the resistome under β-lactam stress, suggesting broader relevance of this recycling module to antibiotic stress responses. (sonnabend2020identificationofdrug pages 2-4)

6) Recent developments (prioritizing 2023–2024)

2024: rapid, no-wash live-cell PG labeling enabled by AmgK/MurU

Hillman et al. (published 2024-03-01) developed a minimalist tetrazine MurNAc (HTz-NAM) probe that is incorporated into PG via AmgK and MurU, enabling fast tetrazine–TCO ligation suitable for live imaging. (hillman2024minimalisttetrazinenacetyl pages 1-2)

Key quantitative advances reported:
- Tz–TCO labeling on bacterial PG: t1/2 = 1.0 ± 0.1 s (EQKU system) (hillman2024minimalisttetrazinenacetyl pages 6-7)
- Labeling kinetics in engineered Bacillus subtilis strain: t1/2 = 1.1 ± 0.3 s (hillman2024minimalisttetrazinenacetyl pages 6-7)
- Growth rescue in the presence of a “lethal dose” of fosfomycin using HTz-NAM: rescue at 0.15 mM for ≥6 h; probe range tested 0.06–6 mM; remodeling performed for three doubling times (60 min) in one workflow. (hillman2024minimalisttetrazinenacetyl pages 4-6)

The authors explicitly show applicability to wild-type P. putida and P. aeruginosa, noting that these pseudomonads “naturally harbor” AmgK/MurU and that labeling in P. putida is improved with reduced background; P. aeruginosa showed high labeling even under basal expression. (hillman2024minimalisttetrazinenacetyl pages 6-7)

7) Current applications and real-world implementations

Chemical biology toolchains for PG biology and antibiotic discovery

The 2024 HTz-NAM approach is positioned as an “exceptional tool” for monitoring PG biosynthesis and enabling new antibiotic screens, in part because kinetics are fast enough to match PG synthesis timescales (minutes). (hillman2024minimalisttetrazinenacetyl pages 1-2)

Potential translational use: pathogen detection in samples

The 2024 study suggests the minimal tetrazine probe could be applied to detect P. aeruginosa in live patient samples, with cystic fibrosis mentioned as a context where outgrowth occurs (proposed application rather than validated clinical deployment). (hillman2024minimalisttetrazinenacetyl pages 6-7)

8) Expert opinions / authoritative analysis

Recycling pathway as antimicrobial target

The mBio 2017 study frames MupP together with AmgK/MurU as determinants of intrinsic fosfomycin resistance and notes that the pathway may serve as a novel target for antimicrobial therapy. (borisova2017thenacetylmuramic pages 1-2, borisova2017thenacetylmuramic pages 9-11)

Clinical microbiology perspective on fosfomycin and Pseudomonas

A 2022 authoritative narrative review emphasizes that Pseudomonas-specific mechanisms (including PG recycling enzymes such as AmgK/MurU) complicate fosfomycin interpretation and that P. aeruginosa-specific breakpoints are not established; EUCAST notes wild-type isolates with ECOFF MIC ~128 mg/L have been treated with combination therapy, and MIC distributions often cluster around 64–128 mg/L. (zheng2022differencesinfosfomycin pages 3-4)

9) Statistics and data highlights (recent studies)

  • Susceptibility shifts when PG salvage is blocked: 4- to 8-fold increased fosfomycin susceptibility reported upon blockade of the salvage pathway in Pseudomonas contexts. (zheng2022differencesinfosfomycin pages 3-4)
  • Fast labeling kinetics enabled by NAM recycling tools (2024): PG-surface Tz–TCO labeling t1/2 ≈ 1 s in engineered systems, enabling real-time imaging without wash steps. (hillman2024minimalisttetrazinenacetyl pages 6-7)
  • Fosfomycin breakpoint context (2022): EUCAST provides no breakpoints for P. aeruginosa but notes ECOFF MIC 128 mg/L and warns against extrapolating E. coli breakpoints; reported ECOFF ranges extend to 512 mg/L in some studies. (zheng2022differencesinfosfomycin pages 3-4)

Evidence-mapped functional synopsis (artifact)

The table below consolidates enzyme function, pathway placement, phenotypes, quantitative values, and key references (with dates/URLs).

Aspect Summary for Pseudomonas putida KT2440 amgK (PP_0405; UniProt Q88QT3) Evidence
Enzyme name / EC AmgK is an N-acetylmuramate/N-acetylglucosamine kinase, also described as an anomeric sugar kinase; UniProt assigns EC 2.7.1.221. In P. putida KT2440 literature, amgK corresponds to PP_0405 and lies adjacent to murU/pp0406. (borisova2017thenacetylmuramic pages 2-4, borisova2017thenacetylmuramic pages 1-2)
Reaction and products AmgK catalyzes C1/anomeric phosphorylation of MurNAc to MurNAc-α-1-phosphate (MurNAc-1P), which MurU then converts to UDP-MurNAc in the salvage pathway. Experimental systems also use AmgK to generate GlcNAc-1P from GlcNAc. (borisova2017thenacetylmuramic pages 2-4, borisova2017thenacetylmuramic pages 1-2, hillman2024minimalisttetrazinenacetyl pages 4-6)
Substrate specificity Primary physiological substrate is MurNAc; later methods papers and pathway descriptions also identify AmgK as MurNAc/GlcNAc kinase and show formation of α-1-phosphorylated products from NAM probes and GlcNAc in vitro. Available retrieved texts support permissive recognition of modified NAM analogs, while detailed kinetic constants specific to P. putida AmgK were not retrieved. (borisova2017thenacetylmuramic pages 1-2, hillman2024minimalisttetrazinenacetyl pages 4-6)
Pathway context AmgK functions in the anabolic peptidoglycan recycling route: AnhMurNAc is processed by AnmK to MurNAc-6P, MupP dephosphorylates to MurNAc, AmgK rephosphorylates at C1 to MurNAc-1P, and MurU forms UDP-MurNAc. This bypasses the MurA/MurB-dependent de novo route targeted by fosfomycin. (borisova2017thenacetylmuramic pages 2-4, borisova2017thenacetylmuramic pages 9-11, zheng2022differencesinfosfomycin pages 3-4)
Cellular localization inference The pathway acts after muropeptide import and cytoplasmic processing; therefore AmgK is inferred to function in the cytoplasm rather than the periplasm or membrane. No direct localization experiment for PP_0405 was retrieved. (borisova2017thenacetylmuramic pages 1-2, borisova2017thenacetylmuramic pages 2-4)
Genetic / phenotypic evidence in P. putida Prior work cited in the mBio 2017 study states that MurNAc accumulates in a ΔamgK mutant of P. putida, consistent with blockage of MurNAc→MurNAc-1P conversion. Deletion of amgK increases fosfomycin susceptibility in P. putida; ortholog complementation across Pseudomonas restores wild-type susceptibility in related studies summarized by reviews. (borisova2017thenacetylmuramic pages 2-4, zheng2022differencesinfosfomycin pages 4-6)
Broader relevance The AmgK–MurU pathway is broadly conserved among many Gram-negative bacteria and contributes to intrinsic fosfomycin resistance by maintaining UDP-MurNAc despite MurA inhibition. Reviews highlight distribution in pathogens such as Pseudomonas, Neisseria, Burkholderia, Brucella, and Legionella. (borisova2017thenacetylmuramic pages 9-11, zheng2022differencesinfosfomycin pages 3-4, ratna2025thelegionellapneumophila pages 16-19)
Real-world applications AmgK/MurU are exploited for metabolic incorporation of MurNAc-derived probes into peptidoglycan. In 2024 live-cell labeling studies, endogenous or heterologous AmgK/MurU enabled rapid, no-wash imaging of PG in P. putida, P. aeruginosa, and engineered strains, with proposed use in antibiotic screening and possibly pathogen detection in patient samples. (hillman2024minimalisttetrazinenacetyl pages 1-2, hillman2024minimalisttetrazinenacetyl pages 6-7, hyland2024synthesisandutilization pages 289-300, hyland2024synthesisandutilization pages 362-370)
Quantitative data available Blocking the salvage pathway yields a reported 4- to 8-fold increase in fosfomycin susceptibility in Pseudomonas spp. Reviews of related recycling enzymes report Km values ~180–1,200 μM and kcat ~5–6 s⁻¹ for AnmK/AmgK/MurK/MurQ ranges, though specific P. putida AmgK values were not retrieved. HTz-NAM/aTCO-SiR labeling on PG showed t1/2 ≈ 1.0 ± 0.1 s in EQKU and 1.1 ± 0.3 s in BSKU; growth rescue under fosfomycin occurred with HTz-NAM as low as 0.15 mM, with probe ranges of 0.06–6 mM tested. (borisova2017thenacetylmuramic pages 9-11, zheng2022differencesinfosfomycin pages 3-4, hillman2024minimalisttetrazinenacetyl pages 6-7, hillman2024minimalisttetrazinenacetyl pages 4-6)
Key references Borisova M, Gisin J, Mayer C. “The N-Acetylmuramic Acid 6-Phosphate Phosphatase MupP Completes the Pseudomonas Peptidoglycan Recycling Pathway Leading to Intrinsic Fosfomycin Resistance.” mBio (May 2017), https://doi.org/10.1128/mbio.00092-17. Hillman AS et al. “Minimalist Tetrazine N-Acetyl Muramic Acid Probes for Rapid and Efficient Labeling of Commensal and Pathogenic Peptidoglycans in Living Bacterial Culture and During Macrophage Invasion.” JACS (Mar 1, 2024), https://doi.org/10.1021/jacs.3c13644. Zheng D et al. “Differences in Fosfomycin Resistance Mechanisms between Pseudomonas aeruginosa and Enterobacterales.” Antimicrob Agents Chemother (Feb 2022), https://doi.org/10.1128/aac.01446-21. Sonnabend MS et al. “Identification of Drug Resistance Determinants in a Clinical Isolate of Pseudomonas aeruginosa by High-Density Transposon Mutagenesis.” Antimicrob Agents Chemother (Feb 21, 2020), https://doi.org/10.1128/AAC.01771-19. (borisova2017thenacetylmuramic pages 2-4, hillman2024minimalisttetrazinenacetyl pages 1-2, zheng2022differencesinfosfomycin pages 3-4, sonnabend2020identificationofdrug pages 1-2)

Table: This table summarizes the verified identity, biochemical role, pathway context, phenotypes, applications, and key citations for amgK/PP_0405 in Pseudomonas putida KT2440. It is useful as a concise evidence map for functional annotation grounded in organism-specific and pathway-level literature.

Limitations of this report (evidence gaps)

  1. Primary 2013 paper not retrieved: UniProt references PubMed:23831760 for AmgK; the original “cell wall recycling shortcut” Nature Chemical Biology paper could not be obtained via the current tool searches. Therefore, this report relies on later peer-reviewed sources (e.g., mBio 2017; JACS 2024) that describe and operationalize the pathway and reaction. (borisova2017thenacetylmuramic pages 2-4, hillman2024minimalisttetrazinenacetyl pages 1-2)
  2. Localization evidence is inferential: No direct AmgK subcellular localization experiment was retrieved; cytosolic localization is inferred from pathway biochemistry and cytosolic fraction metabolite analyses. (borisova2017thenacetylmuramic pages 4-7)
  3. AmgK-specific kinetic/structural parameters in P. putida KT2440 were not found in retrieved full texts; only broader reported ranges for recycling enzymes were available. (borisova2017thenacetylmuramic pages 9-11)

References (URLs and publication dates)

  • Borisova M, Gisin J, Mayer C. mBio. 2017-05. “The N-Acetylmuramic Acid 6-Phosphate Phosphatase MupP Completes the Pseudomonas Peptidoglycan Recycling Pathway Leading to Intrinsic Fosfomycin Resistance.” https://doi.org/10.1128/mbio.00092-17 (borisova2017thenacetylmuramic pages 2-4)
  • Hillman AS et al. J. Am. Chem. Soc. Published 2024-03-01 (received 2023-12-04; revised 2024-02-13; accepted 2024-02-14). “Minimalist Tetrazine N-Acetyl Muramic Acid Probes…” https://doi.org/10.1021/jacs.3c13644 (hillman2024minimalisttetrazinenacetyl pages 1-2)
  • Zheng D et al. Antimicrobial Agents and Chemotherapy. 2022-02. “Differences in Fosfomycin Resistance Mechanisms between Pseudomonas aeruginosa and Enterobacterales.” https://doi.org/10.1128/aac.01446-21 (zheng2022differencesinfosfomycin pages 3-4)
  • Sonnabend MS et al. Antimicrobial Agents and Chemotherapy. Published 2020-02-21. “Identification of Drug Resistance Determinants…” https://doi.org/10.1128/AAC.01771-19 (sonnabend2020identificationofdrug pages 1-2)

References

  1. (borisova2017thenacetylmuramic pages 2-4): Marina Borisova, Jonathan Gisin, and Christoph Mayer. The n -acetylmuramic acid 6-phosphate phosphatase mupp completes the pseudomonas peptidoglycan recycling pathway leading to intrinsic fosfomycin resistance. mBio, May 2017. URL: https://doi.org/10.1128/mbio.00092-17, doi:10.1128/mbio.00092-17. This article has 41 citations and is from a domain leading peer-reviewed journal.

  2. (borisova2017thenacetylmuramic pages 9-11): Marina Borisova, Jonathan Gisin, and Christoph Mayer. The n -acetylmuramic acid 6-phosphate phosphatase mupp completes the pseudomonas peptidoglycan recycling pathway leading to intrinsic fosfomycin resistance. mBio, May 2017. URL: https://doi.org/10.1128/mbio.00092-17, doi:10.1128/mbio.00092-17. This article has 41 citations and is from a domain leading peer-reviewed journal.

  3. (hillman2024minimalisttetrazinenacetyl pages 6-7): Ashlyn S. Hillman, Stephen N. Hyland, Kimberly A. Wodzanowski, DeVonte L. Moore, Sushanta Ratna, Andrew Jemas, Liam-Michael D. Sandles, Timothy Chaya, Arit Ghosh, Joseph M. Fox, and Catherine L. Grimes. Minimalist tetrazine n-acetyl muramic acid probes for rapid and efficient labeling of commensal and pathogenic peptidoglycans in living bacterial culture and during macrophage invasion. Journal of the American Chemical Society, 146:6817-6829, Mar 2024. URL: https://doi.org/10.1021/jacs.3c13644, doi:10.1021/jacs.3c13644. This article has 29 citations and is from a highest quality peer-reviewed journal.

  4. (hillman2024minimalisttetrazinenacetyl pages 4-6): Ashlyn S. Hillman, Stephen N. Hyland, Kimberly A. Wodzanowski, DeVonte L. Moore, Sushanta Ratna, Andrew Jemas, Liam-Michael D. Sandles, Timothy Chaya, Arit Ghosh, Joseph M. Fox, and Catherine L. Grimes. Minimalist tetrazine n-acetyl muramic acid probes for rapid and efficient labeling of commensal and pathogenic peptidoglycans in living bacterial culture and during macrophage invasion. Journal of the American Chemical Society, 146:6817-6829, Mar 2024. URL: https://doi.org/10.1021/jacs.3c13644, doi:10.1021/jacs.3c13644. This article has 29 citations and is from a highest quality peer-reviewed journal.

  5. (zheng2022differencesinfosfomycin pages 3-4): Dina Zheng, Phillip J. Bergen, Cornelia B. Landersdorfer, and Elizabeth B. Hirsch. Differences in fosfomycin resistance mechanisms between pseudomonas aeruginosa and enterobacterales. Feb 2022. URL: https://doi.org/10.1128/aac.01446-21, doi:10.1128/aac.01446-21. This article has 43 citations and is from a highest quality peer-reviewed journal.

  6. (borisova2017thenacetylmuramic pages 4-7): Marina Borisova, Jonathan Gisin, and Christoph Mayer. The n -acetylmuramic acid 6-phosphate phosphatase mupp completes the pseudomonas peptidoglycan recycling pathway leading to intrinsic fosfomycin resistance. mBio, May 2017. URL: https://doi.org/10.1128/mbio.00092-17, doi:10.1128/mbio.00092-17. This article has 41 citations and is from a domain leading peer-reviewed journal.

  7. (zheng2022differencesinfosfomycin pages 4-6): Dina Zheng, Phillip J. Bergen, Cornelia B. Landersdorfer, and Elizabeth B. Hirsch. Differences in fosfomycin resistance mechanisms between pseudomonas aeruginosa and enterobacterales. Feb 2022. URL: https://doi.org/10.1128/aac.01446-21, doi:10.1128/aac.01446-21. This article has 43 citations and is from a highest quality peer-reviewed journal.

  8. (sonnabend2020identificationofdrug pages 2-4): Michael S. Sonnabend, Kristina Klein, Sina Beier, Angel Angelov, Robert Kluj, Christoph Mayer, Caspar Groß, Kathrin Hofmeister, Antonia Beuttner, Matthias Willmann, Silke Peter, Philipp Oberhettinger, Annika Schmidt, Ingo B. Autenrieth, Monika Schütz, and Erwin Bohn. Identification of drug resistance determinants in a clinical isolate of pseudomonas aeruginosa by high-density transposon mutagenesis. Feb 2020. URL: https://doi.org/10.1128/aac.01771-19, doi:10.1128/aac.01771-19. This article has 42 citations and is from a highest quality peer-reviewed journal.

  9. (hillman2024minimalisttetrazinenacetyl pages 1-2): Ashlyn S. Hillman, Stephen N. Hyland, Kimberly A. Wodzanowski, DeVonte L. Moore, Sushanta Ratna, Andrew Jemas, Liam-Michael D. Sandles, Timothy Chaya, Arit Ghosh, Joseph M. Fox, and Catherine L. Grimes. Minimalist tetrazine n-acetyl muramic acid probes for rapid and efficient labeling of commensal and pathogenic peptidoglycans in living bacterial culture and during macrophage invasion. Journal of the American Chemical Society, 146:6817-6829, Mar 2024. URL: https://doi.org/10.1021/jacs.3c13644, doi:10.1021/jacs.3c13644. This article has 29 citations and is from a highest quality peer-reviewed journal.

  10. (borisova2017thenacetylmuramic pages 1-2): Marina Borisova, Jonathan Gisin, and Christoph Mayer. The n -acetylmuramic acid 6-phosphate phosphatase mupp completes the pseudomonas peptidoglycan recycling pathway leading to intrinsic fosfomycin resistance. mBio, May 2017. URL: https://doi.org/10.1128/mbio.00092-17, doi:10.1128/mbio.00092-17. This article has 41 citations and is from a domain leading peer-reviewed journal.

  11. (ratna2025thelegionellapneumophila pages 16-19): Sushanta Ratna, Lina Pradhan, Marina P. Vasconcelos, Aastha Acharya, Bella Carnahan, Alex Wang, Arit Ghosh, Abigail Bolt, Jacob Ellis, Stephen N. Hyland, Ashlyn S. Hillman, Joseph M. Fox, April Kloxin, M. Ramona Neunuebel, and Catherine Leimkuhler Grimes. The legionella pneumophila peptidoglycan recycling kinase, amgk, is essential for survival and replication inside host alveolar macrophages. bioRxiv, Mar 2025. URL: https://doi.org/10.1101/2025.03.21.644609, doi:10.1101/2025.03.21.644609. This article has 4 citations.

  12. (hyland2024synthesisandutilization pages 289-300): SN Hyland. Synthesis and utilization of n-acetyl muramic acid derivatives as tools for probing information about peptidoglycan structure, biogenesis and immunological …. Unknown journal, 2024.

  13. (hyland2024synthesisandutilization pages 362-370): SN Hyland. Synthesis and utilization of n-acetyl muramic acid derivatives as tools for probing information about peptidoglycan structure, biogenesis and immunological …. Unknown journal, 2024.

  14. (sonnabend2020identificationofdrug pages 1-2): Michael S. Sonnabend, Kristina Klein, Sina Beier, Angel Angelov, Robert Kluj, Christoph Mayer, Caspar Groß, Kathrin Hofmeister, Antonia Beuttner, Matthias Willmann, Silke Peter, Philipp Oberhettinger, Annika Schmidt, Ingo B. Autenrieth, Monika Schütz, and Erwin Bohn. Identification of drug resistance determinants in a clinical isolate of pseudomonas aeruginosa by high-density transposon mutagenesis. Feb 2020. URL: https://doi.org/10.1128/aac.01771-19, doi:10.1128/aac.01771-19. This article has 42 citations and is from a highest quality peer-reviewed journal.

Artifacts

Citations

  1. borisova2017thenacetylmuramic pages 2-4
  2. hillman2024minimalisttetrazinenacetyl pages 4-6
  3. borisova2017thenacetylmuramic pages 9-11
  4. zheng2022differencesinfosfomycin pages 3-4
  5. sonnabend2020identificationofdrug pages 2-4
  6. hillman2024minimalisttetrazinenacetyl pages 1-2
  7. hillman2024minimalisttetrazinenacetyl pages 6-7
  8. borisova2017thenacetylmuramic pages 4-7
  9. sonnabend2020identificationofdrug pages 1-2
  10. zheng2022differencesinfosfomycin pages 4-6
  11. borisova2017thenacetylmuramic pages 1-2
  12. ratna2025thelegionellapneumophila pages 16-19
  13. hyland2024synthesisandutilization pages 289-300
  14. hyland2024synthesisandutilization pages 362-370
  15. https://doi.org/10.1128/mbio.00092-17.
  16. https://doi.org/10.1021/jacs.3c13644.
  17. https://doi.org/10.1128/aac.01446-21.
  18. https://doi.org/10.1128/AAC.01771-19.
  19. https://doi.org/10.1128/mbio.00092-17
  20. https://doi.org/10.1021/jacs.3c13644
  21. https://doi.org/10.1128/aac.01446-21
  22. https://doi.org/10.1128/AAC.01771-19
  23. https://doi.org/10.1128/mbio.00092-17,
  24. https://doi.org/10.1021/jacs.3c13644,
  25. https://doi.org/10.1128/aac.01446-21,
  26. https://doi.org/10.1128/aac.01771-19,
  27. https://doi.org/10.1101/2025.03.21.644609,

📄 View Raw YAML

 
id: Q88QT3
gene_symbol: amgK
product_type: PROTEIN
status: DRAFT
taxon:
  id: NCBITaxon:160488
  label: Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)
description: amgK encodes an ATP-dependent MurNAc/GlcNAc kinase in peptidoglycan recycling and intrinsic fosfomycin resistance.
existing_annotations:
- term:
    id: GO:0009254
    label: peptidoglycan turnover
  evidence_type: IEA
  original_reference_id: GO_REF:0000041
  review:
    summary: The IEA peptidoglycan turnover row captures AmgK's recycling-pathway role.
    action: ACCEPT
    reason: UniProt and the experimental paper place AmgK in a peptidoglycan recycling shortcut.
    supported_by:
    - reference_id: file:PSEPK/amgK/amgK-uniprot.txt
      supporting_text: Is involved in peptidoglycan recycling
    - reference_id: file:PSEPK/amgK/amgK-goa.tsv
      supporting_text: "GO:0009254\tpeptidoglycan turnover"
    - reference_id: file:PSEPK/amgK/amgK-deep-research-falcon.md
      supporting_text: |-
        phosphorylates **N-acetylmuramic acid (MurNAc/NAM)** at the **anomeric carbon (C1)** to produce **MurNAc-α-1-phosphate (MurNAc-1P)**, a committed intermediate of a **MurU-dependent anabolic peptidoglycan (PG) recycling pathway** that regenerates **UDP-MurNAc** for cell wall synthesis.
- term:
    id: GO:0005524
    label: ATP binding
  evidence_type: IDA
  original_reference_id: PMID:23831760
  review:
    summary: ATP binding is necessary for the kinase reaction but is not the informative molecular function.
    action: KEEP_AS_NON_CORE
    reason: The core annotation should be kinase activity on MurNAc/GlcNAc substrates.
    supported_by:
    - reference_id: file:PSEPK/amgK/amgK-uniprot.txt
      supporting_text: ATP-dependent phosphorylation
    - reference_id: file:PSEPK/amgK/amgK-goa.tsv
      supporting_text: "GO:0005524\tATP binding"
- term:
    id: GO:0009254
    label: peptidoglycan turnover
  evidence_type: IMP
  original_reference_id: PMID:23831760
  review:
    summary: The IMP peptidoglycan turnover row is experimentally supported and should be retained.
    action: ACCEPT
    reason: The AmgK/MurU pathway bypasses de novo UDP-MurNAc synthesis and contributes to peptidoglycan recycling.
    supported_by:
    - reference_id: PMID:23831760
      supporting_text: channeling external MurNAc directly to peptidoglycan biosynthesis
    - reference_id: file:PSEPK/amgK/amgK-goa.tsv
      supporting_text: "GO:0009254\tpeptidoglycan turnover"
    - reference_id: file:PSEPK/amgK/amgK-deep-research-falcon.md
      supporting_text: |-
        A key organism-specific observation in *P. putida* is that **MurNAc accumulates in a ΔamgK mutant**, consistent with AmgK being required to phosphorylate MurNAc in the salvage route.
    - reference_id: file:PSEPK/amgK/amgK-deep-research-falcon.md
      supporting_text: |-
        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.
- term:
    id: GO:0019200
    label: carbohydrate kinase activity
  evidence_type: IDA
  original_reference_id: PMID:23831760
  review:
    summary: Carbohydrate kinase activity is correct but too broad for AmgK's substrate-specific activity.
    action: MARK_AS_OVER_ANNOTATED
    reason: AmgK specifically phosphorylates N-acetylmuramate and N-acetylglucosamine at C1; GOA lacks a specific MurNAc/GlcNAc kinase term, which is requested below in proposed_new_terms.
    supported_by:
    - reference_id: file:PSEPK/amgK/amgK-uniprot.txt
      supporting_text: phosphorylation of N-acetylmuramate (MurNAc) and N-acetylglucosamine
    - reference_id: file:PSEPK/amgK/amgK-goa.tsv
      supporting_text: "GO:0019200\tcarbohydrate kinase activity"
    - reference_id: file:PSEPK/amgK/amgK-deep-research-falcon.md
      supporting_text: |-
        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.
- term:
    id: GO:0097172
    label: N-acetylmuramic acid metabolic process
  evidence_type: IDA
  original_reference_id: PMID:23831760
  review:
    summary: N-acetylmuramic acid metabolism is directly supported by AmgK's MurNAc phosphorylation reaction.
    action: ACCEPT
    reason: The enzyme phosphorylates MurNAc to MurNAc alpha-1-phosphate in the cell-wall recycling pathway.
    supported_by:
    - reference_id: file:PSEPK/amgK/amgK-uniprot.txt
      supporting_text: leading to MurNAc alpha-1P
    - reference_id: file:PSEPK/amgK/amgK-goa.tsv
      supporting_text: "GO:0097172\tN-acetylmuramic acid metabolic process"
    - reference_id: file:PSEPK/amgK/amgK-deep-research-falcon.md
      supporting_text: |-
        phosphorylates **N-acetylmuramic acid (MurNAc/NAM)** at the **anomeric carbon (C1)** to produce **MurNAc-α-1-phosphate (MurNAc-1P)**, a committed intermediate of a **MurU-dependent anabolic peptidoglycan (PG) recycling pathway** that regenerates **UDP-MurNAc** for cell wall synthesis.
references:
- id: GO_REF:0000041
  title: Gene Ontology annotation based on UniPathway vocabulary mapping
  findings: []
- id: PMID:23831760
  title: A cell wall recycling shortcut that bypasses peptidoglycan de novo biosynthesis.
  findings: []
- id: file:PSEPK/amgK/amgK-uniprot.txt
  title: UniProtKB reviewed entry for amgK
  findings:
  - statement: UniProt provides the reviewed functional description used for the amgK review.
- id: file:PSEPK/amgK/amgK-goa.tsv
  title: QuickGO GOA annotations for amgK
  findings:
  - statement: The fetched GOA table contains the annotations reviewed for amgK.
- id: file:interpro/panther/PTHR33540/PTHR33540-metadata.yaml
  title: PANTHER family metadata for amgK
  findings:
  - statement: PANTHER places AmgK in the anomeric sugar kinase clade of the TsaE/AmgK kinase family.
- id: file:PSEPK/amgK/amgK-deep-research-falcon.md
  title: Falcon (Edison Scientific) deep research report on amgK (PP_0405; Q88QT3)
  findings:
  - statement: |-
      AmgK phosphorylates MurNAc at the anomeric carbon (C1) to produce MurNAc-alpha-1-phosphate, the committed intermediate of the MurU-dependent anabolic peptidoglycan recycling pathway.
    supporting_text: |-
      phosphorylates **N-acetylmuramic acid (MurNAc/NAM)** at the **anomeric carbon (C1)** to produce **MurNAc-α-1-phosphate (MurNAc-1P)**, a committed intermediate of a **MurU-dependent anabolic peptidoglycan (PG) recycling pathway** that regenerates **UDP-MurNAc** for cell wall synthesis.
  - statement: |-
      The recycling pathway bypasses the de novo MurA/MurB route and confers intrinsic fosfomycin resistance, since fosfomycin targets MurA.
    supporting_text: |-
      This recycling “shortcut” bypasses the canonical **MurA/MurB** de novo pathway and contributes to **intrinsic fosfomycin resistance** in pseudomonads because fosfomycin targets MurA.
  - statement: |-
      AmgK is an anomeric MurNAc/GlcNAc kinase generating C1-phosphorylated sugars from both MurNAc and GlcNAc.
    supporting_text: |-
      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.
  - statement: |-
      MurNAc accumulates in a P. putida amgK deletion mutant, confirming AmgK is required for the MurNAc phosphorylation step of the salvage route.
    supporting_text: |-
      A key organism-specific observation in *P. putida* is that **MurNAc accumulates in a ΔamgK mutant**, consistent with AmgK being required to phosphorylate MurNAc in the salvage route.
  - statement: |-
      AmgK acts downstream of MupP in the anabolic recycling route, converting MurNAc to MurNAc-1P for MurU to form UDP-MurNAc.
    supporting_text: |-
      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.
  - statement: |-
      AmgK is inferred to act in the cytoplasm, consistent with the cytosolic processing of imported peptidoglycan fragments.
    supporting_text: |-
      This supports the inference that AmgK functions in the **cytoplasm**.
core_functions:
- description: ATP-dependent MurNAc/GlcNAc kinase that channels recycled cell-wall sugars into peptidoglycan precursor metabolism; no exact current GO molecular-function term exists, so the specific activity is requested in proposed_new_terms.
  directly_involved_in:
  - id: GO:0009254
    label: peptidoglycan turnover
  - id: GO:0097172
    label: N-acetylmuramic acid metabolic process
  supported_by:
  - reference_id: file:PSEPK/amgK/amgK-uniprot.txt
    supporting_text: phosphorylation of N-acetylmuramate (MurNAc) and N-acetylglucosamine
  - reference_id: PMID:23831760
    supporting_text: anomeric sugar kinase AmgK
  - reference_id: file:PSEPK/amgK/amgK-deep-research-falcon.md
    supporting_text: |-
      phosphorylates **N-acetylmuramic acid (MurNAc/NAM)** at the **anomeric carbon (C1)** to produce **MurNAc-α-1-phosphate (MurNAc-1P)**, a committed intermediate of a **MurU-dependent anabolic peptidoglycan (PG) recycling pathway** that regenerates **UDP-MurNAc** for cell wall synthesis.
  - reference_id: file:PSEPK/amgK/amgK-deep-research-falcon.md
    supporting_text: |-
      This recycling “shortcut” bypasses the canonical **MurA/MurB** de novo pathway and contributes to **intrinsic fosfomycin resistance** in pseudomonads because fosfomycin targets MurA.
proposed_new_terms:
- proposed_name: N-acetylmuramate/N-acetylglucosamine kinase activity
  proposed_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.
  proposed_parent:
    id: GO:0019200
    label: carbohydrate kinase activity
  supported_by:
  - reference_id: file:PSEPK/amgK/amgK-uniprot.txt
    supporting_text: Sugar kinase that catalyzes the ATP-dependent phosphorylation
  - reference_id: file:PSEPK/amgK/amgK-uniprot.txt
    supporting_text: N-acetylmuramate (MurNAc) and N-acetylglucosamine
  - reference_id: file:PSEPK/amgK/amgK-deep-research-falcon.md
    supporting_text: |-
      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.
suggested_questions:
- question: What are the in vivo relative contributions of MurNAc, GlcNAc, and GalNAc phosphorylation by AmgK during KT2440 cell-wall recycling?
suggested_experiments:
- description: Compare sugar-phosphate metabolite levels and fosfomycin sensitivity in wild-type, amgK knockout, and catalytic-site rescue strains.
  experiment_type: metabolomics and antibiotic sensitivity assay