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this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.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.
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)
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)
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)
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)
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)
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
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)
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)
The pathway paper reports that bioinformatic searches in pseudomonad genomes identified murU (pp0406) and the adjacent gene pp0405 (amgK). (borisova2017thenacetylmuramic pages 2-4)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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.
References
(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.
(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.
(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.
(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.
(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.
(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.
(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.
(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.
(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.
(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.
(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.
(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.
(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.
(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.