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protein_family: Belongs to the YjdM family. .
protein_domains: YjdM. (IPR004624); YjdM_C. (IPR013988); YjdM_N. (IPR013987); YjdM
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Question

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.

Target Gene/Protein Identity (from UniProt):

• UniProt Accession: P0AFJ1
• Protein Description: RecName: Full=Phosphonoacetate hydrolase YjdM {ECO:0000303|PubMed:37963869}; EC=3.11.1.2 {ECO:0000269|PubMed:37963869};
• Gene Information: Name=yjdM; Synonyms=phnA {ECO:0000303|PubMed:2155230}; OrderedLocusNames=b4108, JW4069;
• Organism (full): Escherichia coli (strain K12).
• Protein Family: Belongs to the YjdM family. .
• Key Domains: YjdM. (IPR004624); YjdM_C. (IPR013988); YjdM_N. (IPR013987); YjdM (PF03831); Zn_Ribbon_YjdM (PF08274)

MANDATORY VERIFICATION STEPS:

1. Check if the gene symbol "yjdM" matches the protein description above
2. Verify the organism is correct: Escherichia coli (strain K12).
3. Check if protein family/domains align with what you find in literature
4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'yjdM' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information

Research Target:

Please provide a comprehensive research report on the gene yjdM (gene ID: yjdM, UniProt: P0AFJ1) in ECOLI.

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this with annotations you find in gene/protein databases, but these can be outdated or inaccurate.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.

Output

Question: You are an expert researcher providing comprehensive, well-cited information.

Provide detailed information focusing on:
1. Key concepts and definitions with current understanding
2. Recent developments and latest research (prioritize 2023-2024 sources)
3. Current applications and real-world implementations
4. Expert opinions and analysis from authoritative sources
5. Relevant statistics and data from recent studies

Format as a comprehensive research report with proper citations. Include URLs and publication dates where available.
Always prioritize recent, authoritative sources and provide specific citations for all major claims.

Gene Research for Functional Annotation

⚠️ CRITICAL: Gene/Protein Identification Context

BEFORE YOU BEGIN RESEARCH: You MUST verify you are researching the CORRECT gene/protein. Gene symbols can be ambiguous, especially for less well-characterized genes from non-model organisms.

Target Gene/Protein Identity (from UniProt):

• UniProt Accession: P0AFJ1
• Protein Description: RecName: Full=Phosphonoacetate hydrolase YjdM {ECO:0000303|PubMed:37963869}; EC=3.11.1.2 {ECO:0000269|PubMed:37963869};
• Gene Information: Name=yjdM; Synonyms=phnA {ECO:0000303|PubMed:2155230}; OrderedLocusNames=b4108, JW4069;
• Organism (full): Escherichia coli (strain K12).
• Protein Family: Belongs to the YjdM family. .
• Key Domains: YjdM. (IPR004624); YjdM_C. (IPR013988); YjdM_N. (IPR013987); YjdM (PF03831); Zn_Ribbon_YjdM (PF08274)

MANDATORY VERIFICATION STEPS:

1. Check if the gene symbol "yjdM" matches the protein description above
2. Verify the organism is correct: Escherichia coli (strain K12).
3. Check if protein family/domains align with what you find in literature
4. If you find literature for a DIFFERENT gene with the same or similar symbol, STOP

If Gene Symbol is Ambiguous or You Cannot Find Relevant Literature:

DO NOT PROCEED WITH RESEARCH ON A DIFFERENT GENE. Instead:
- State clearly: "The gene symbol 'yjdM' is ambiguous or literature is limited for this specific protein"
- Explain what you found (e.g., "Found extensive literature on a different gene with the same symbol in a different organism")
- Describe the protein based ONLY on the UniProt information provided above
- Suggest that the protein function can be inferred from domain/family information

Research Target:

Please provide a comprehensive research report on the gene yjdM (gene ID: yjdM, UniProt: P0AFJ1) in ECOLI.

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 E. coli K-12 yjdM (UniProt P0AFJ1)

Executive summary

The Escherichia coli K-12 gene yjdM (UniProt P0AFJ1; locus b4108/JW4069) is explicitly reported in E. coli literature as formerly named phnA, and is distinct from the canonical E. coli phn C–P lyase operon that enables broad phosphonate utilization under phosphate starvation. (smithfrieday2022deletionofprou pages 5-8, ruffolo2023themicrobialdegradation pages 8-10)

A major recent advance (2023) is the direct biochemical validation that purified E. coli K-12 MG1655 YjdM exhibits phosphonoacetate hydrolase activity (EC 3.11.1.2) on phosphonoacetate in vitro, providing strong evidence for its catalytic potential. (kim2023functionalannotationof pages 6-7, kim2023functionalannotationof media 4546f8e8)

However, the physiological role in vivo (true native substrate(s), pathway membership, and conditions where it contributes to growth/fitness) remains uncertain, and some analyses emphasize that genomic context in E. coli is atypical relative to bona fide phosphonoacetate-utilization modules found in other bacteria. (crecylagard2025limitationsofcurrent pages 7-9)

1) Key concepts and definitions (current understanding)

1.1 Phosphonates and C–P bond cleavage

Phosphonates are organophosphorus compounds containing a chemically stable carbon–phosphorus (C–P) bond. Microbes have evolved multiple strategies to access phosphorus from phosphonates, and these strategies are often categorized by the ultimate C–P cleavage mechanism: (i) hydrolytic, (ii) oxidative, and (iii) radical (C–P lyase). (ruffolo2023themicrobialdegradation pages 2-4)

1.2 Phosphonoacetate hydrolase activity (EC 3.11.1.2)

Phosphonoacetate hydrolase (often called PhnA in organisms that use the phosphonoacetate pathway) catalyzes hydrolysis of phosphonoacetate to acetate and inorganic phosphate (Pi). (agarwal2011structuralandmechanistic pages 1-2, kamat2013theenzymaticconversion pages 2-4)

Mechanistically, characterized PhnA enzymes belong to the alkaline phosphatase superfamily and typically employ a binuclear metal center and a conserved threonine nucleophile that forms a covalent phospho-enzyme intermediate, broadly analogous to alkaline phosphatase/nucleotide pyrophosphatase chemistry, but with the unusual feature that the leaving group corresponds to an enolate stabilized by the substrate’s β-carbonyl system. (peck2013phosphonatebiosynthesisand pages 6-7, agarwal2011structuralandmechanistic pages 4-5, kamat2013theenzymaticconversion pages 2-4)

2) Verification of the correct gene/protein identity (critical disambiguation)

• Organism and locus context: The target is yjdM in E. coli K-12 (UniProt P0AFJ1 per user). A E. coli genomic/neighborhood discussion explicitly states “yjdM (formerly phnA)” and places yjdM among conserved genes upstream of proP, together with yjdN (formerly phnB). (smithfrieday2022deletionofprou pages 5-8)
• Functional identity: A 2023 peer‑reviewed study using E. coli K-12 MG1655 purified protein assays reports phosphonoacetate hydrolase activity for YjdM, supporting that the symbol yjdM here refers to the protein with EC 3.11.1.2 activity. (kim2023functionalannotationof pages 6-7, kim2023functionalannotationof media 4546f8e8)

Together, these sources support that the report is addressing the intended E. coli K-12 YjdM/P0AFJ1 target rather than a different “yjdM” in another organism. (smithfrieday2022deletionofprou pages 5-8, kim2023functionalannotationof pages 6-7)

3) Primary molecular function: reaction, substrate specificity, and mechanistic inferences

3.1 Reaction catalyzed

The enzyme activity assigned to YjdM is phosphonoacetate hydrolase (EC 3.11.1.2), i.e. hydrolysis of phosphonoacetate to acetate + inorganic phosphate. This is the canonical reaction catalyzed by PhnA enzymes characterized in other bacteria (e.g., Sinorhizobium meliloti, Pseudomonas fluorescens), and is also the function experimentally supported for the E. coli YjdM protein in vitro. (agarwal2011structuralandmechanistic pages 1-2, kamat2013theenzymaticconversion pages 2-4, kim2023functionalannotationof pages 6-7)

3.2 Experimental evidence in E. coli (2023)

Kim et al. (published Nov 2023) predicted YjdM as EC 3.11.1.2 and reported that purified E. coli K‑12 MG1655 YjdM displays specific phosphonoacetate hydrolase activity = 139.85 U·mg⁻1, as shown in their Figure 4b. (kim2023functionalannotationof pages 6-7, kim2023functionalannotationof media 4546f8e8)

The same paper contrasts this value with a previously reported specific activity for phosphonoacetate hydrolase from Pseudomonas fluorescens 23F (60 U·mg⁻1), indicating that the measured in vitro activity of E. coli YjdM is at least comparable to (and in that comparison higher than) a known phosphonoacetate hydrolase benchmark. (kim2023functionalannotationof pages 6-7)

3.3 Substrate specificity (what is known vs unknown)

Direct E. coli YjdM substrate scope was not comprehensively enumerated in the retrieved main-text evidence; the strongest direct result available here is activity on phosphonoacetate. (kim2023functionalannotationof pages 6-7)

For bona fide PhnA enzymes, detailed substrate/inhibitor profiling indicates:
* High activity for phosphonoacetate (catalytic efficiency kcat/Km ≈ 4 × 10^4 M⁻1 s⁻1 at pH 7, 30 °C). (kim2011divergenceofchemical pages 7-9)
* Much lower turnover for phosphonoacetaldehyde compared with phosphonoacetate, and lack of detectable turnover on some other tested phosphonates such as fosfomycin and phosphonopyruvate under the assay conditions described. (kim2011divergenceofchemical pages 7-9)
* Competitive inhibition by phosphonate analogs including phosphonopropionate and phosphonoformate (Ki values reported). (kim2011divergenceofchemical pages 7-9)

These biochemical benchmarks support a view that phosphonoacetate hydrolases are typically specialized enzymes, and provide expectations for what might be tested for E. coli YjdM in future work; however, such specificity claims should not be assumed for YjdM without direct profiling. (kim2011divergenceofchemical pages 7-9, crecylagard2025limitationsofcurrent pages 7-9)

3.4 Mechanism and catalytic features (inference from characterized PhnA enzymes)

Multiple structural/mechanistic studies of phosphonoacetate hydrolase (PhnA/PAH) support common mechanistic themes:
* Catalytic threonine functions as the nucleophile (e.g., Thr64/Thr68 depending on sequence numbering), consistent with a covalent phospho-enzyme intermediate. (kim2011divergenceofchemical pages 1-2, agarwal2011structuralandmechanistic pages 4-5)
* A dinuclear/bimetal active site is present (often described with two Zn ions in structures). (agarwal2011structuralandmechanistic pages 6-8, kamat2013theenzymaticconversion pages 2-4)
* Metal dependence: in one detailed kinetic analysis, 3 mM Zn2+ increased initial velocity ~10-fold relative to metal-depleted enzyme, and Zn was used as activator for kinetic measurements. (kim2011divergenceofchemical pages 7-9)
* Proposed leaving-group stabilization involves metal coordination and/or conserved Lys residues (e.g., Lys126/Lys128 implicated in one study) and features unique relative to typical alkaline phosphatase reactions because the leaving group is carbon-centered (enolate/aci-carboxylate) rather than an oxyanion. (peck2013phosphonatebiosynthesisand pages 6-7, kim2011divergenceofchemical pages 1-2)

These mechanistic conclusions are strongest for PhnA enzymes from organisms where the phosphonoacetate pathway is genetically and physiologically established; they are best treated as mechanistic context for YjdM rather than as directly proven for E. coli YjdM, unless YjdM is shown to be homologous and experimentally similar at the active-site level. (crecylagard2025limitationsofcurrent pages 7-9, agarwal2011structuralandmechanistic pages 6-8)

4) Biological role, pathways, and regulation in E. coli (and why interpretation is nuanced)

4.1 The canonical E. coli phosphonate utilization system: C–P lyase (phn operon)

In E. coli, phosphonate utilization is classically attributed to the C–P lyase system. A 2023 review summarizes that E. coli C–P lyase genes are encoded by the 14‑gene phnCDEFGHIJLKMNOP operon and are induced by phosphorus limitation under Pho regulon control. (ruffolo2023themicrobialdegradation pages 8-10)

The foundational genetic work (Metcalf & Wanner; published Jan 1991) found that the phn locus is PhoB/PhoR dependent and is induced roughly ~100‑fold under phosphate limitation, consistent with a phosphate-starvation response. (metcalf1991involvementofthe pages 11-11)

Importantly, Metcalf & Wanner also report that while a larger region contained ORFs designated phnA–phnQ, genetic analyses supported phnC–phnP as the complete set required for phosphonate utilization—implying that phnA is not essential for the canonical E. coli phosphonate utilization phenotype. (metcalf1991involvementofthe pages 11-11)

4.2 PhnA/PhnWAY-type hydrolytic phosphonate catabolism (comparative context)

Outside E. coli, the hydrolytic PhnWAY route can degrade 2‑aminoethylphosphonate (AEP) by converting it via transamination (PhnW) to phosphonoacetaldehyde, oxidation (PhnY) to phosphonoacetate, and finally hydrolysis by PhnA to liberate phosphate. (agarwal2014structureandfunction pages 1-2, ruffolo2023themicrobialdegradation pages 5-7)

The 2023 review further notes that phosphonoacetate hydrolase pathways may be substrate-inducible and phosphate-independent in some organisms (contrasting with Pho-regulated C–P lyase). (ruffolo2023themicrobialdegradation pages 16-17)

4.3 Reconciling E. coli yjdM (formerly phnA) with pathway biology

A key tension is that E. coli yjdM is historically called phnA, yet the main established E. coli phosphonate assimilation system is the Pho‑regulated phnCDE…P C–P lyase operon. (metcalf1991involvementofthe pages 11-11, ruffolo2023themicrobialdegradation pages 8-10)

A later analysis highlights that although YjdM has in vitro phosphonoacetate hydrolase activity, genomic context and comparative neighborhood evidence suggest that E. coli yjdM is not embedded in a typical phosphonoacetate utilization module, and earlier claims that E. coli possesses functional phosphonoacetate hydrolase activity in vivo may not hold; thus, the physiological pathway role remains unresolved. (crecylagard2025limitationsofcurrent pages 7-9)

Taken together, the most evidence-supported statement at present is:
YjdM from E. coli K‑12 can catalyze phosphonoacetate hydrolysis in vitro, but its native substrate(s) and contribution to phosphonate assimilation in vivo in E. coli are not yet firmly established. (kim2023functionalannotationof pages 6-7, crecylagard2025limitationsofcurrent pages 7-9)

5) Cellular localization and where the reaction occurs

Direct experimental localization (e.g., fractionation, microscopy) for E. coli YjdM was not identified in the retrieved sources. (kim2023functionalannotationof pages 6-7, crecylagard2025limitationsofcurrent pages 7-9)

Nonetheless, based on the fact that phosphonoacetate hydrolase/PhnA enzymes are characterized as soluble metalloenzymes acting on small cytosolic metabolites in hydrolytic phosphonate pathways, the most plausible working model is that YjdM acts intracellularly (cytosol), downstream of transport of phosphonates/phosphonoacetate or generation of phosphonoacetate from other intermediates. This inference should be treated as provisional until E. coli-specific localization evidence is produced. (kamat2013theenzymaticconversion pages 2-4, ruffolo2023themicrobialdegradation pages 5-7)

6) Applications and real-world implementations

6.1 Environmental phosphorus cycling and biodegradation

Microbial phosphonate catabolism is environmentally significant because it mobilizes phosphorus from chemically stable organophosphorus pools. Pathways involving PhnA are discussed as widespread and relevant to phosphonate turnover in nature, with implications for nutrient cycling and pollutant degradation strategies. (ruffolo2023themicrobialdegradation pages 5-7, ruffolo2023themicrobialdegradation pages 2-4)

6.2 Biosensing of phosphonoacetate (biotechnology)

A practical biotechnology implementation is the construction of a whole-cell biosensor for phosphonoacetate, using the LysR-type regulator PhnR and the phosphonoacetate degradative promoter from Pseudomonas fluorescens 23F, deployed in E. coli DH5α as a host chassis. This biosensor detected phosphonoacetate at threshold concentrations as low as 0.5 μM, which was reported as ~100× lower than non-biological analytical detection limits at the time. (kulakova2009theconstructionof; retrieved but not evidence-extracted here)

While this biosensor does not directly involve E. coli yjdM, it illustrates real-world use of the phosphonoacetate utilization regulon and provides a concrete implementation relevant to phosphonoacetate hydrolase pathways. (kulakova2009theconstructionof)

7) Expert opinions, analysis, and current uncertainties

7.1 Expert synthesis of pathway diversity (2023 review)

The 2023 review by Ruffolo et al. emphasizes that hydrolytic and oxidative phosphonate catabolic systems are often substrate-specific, whereas C–P lyase is broad-spectrum; it also stresses the importance of gene clustering and regulation in interpreting function from genomes. This framing is directly relevant to interpreting yjdM in E. coli, where gene neighborhood and regulatory logic differ from prototypical PhnA modules. (ruffolo2023themicrobialdegradation pages 2-4, ruffolo2023themicrobialdegradation pages 8-10)

7.2 Caution on assigning physiological roles from in vitro activity alone

A later critical analysis (preprint context) uses yjdM as an example where activity can be shown in vitro but genomic context comparisons complicate the conclusion that the enzyme participates in the expected physiological pathway in vivo in E. coli. This underscores that functional annotation benefits from integrating biochemical assays with genetics, physiology, and comparative genomics. (crecylagard2025limitationsofcurrent pages 7-9)

8) Key statistics and data points (recent + foundational)

• YjdM (E. coli K‑12 MG1655) in vitro specific activity on phosphonoacetate: 139.85 U·mg⁻1 (Kim et al., 2023-11, Nature Communications). (kim2023functionalannotationof pages 6-7, kim2023functionalannotationof media 4546f8e8)
• Reference PAH (Pseudomonas fluorescens 23F) specific activity (as compared in 2023 paper): 60 U·mg⁻1. (kim2023functionalannotationof pages 6-7)
• Catalytic efficiency benchmark for phosphonoacetate hydrolase (characterized enzyme): kcat/Km ≈ 4 × 10^4 M⁻1 s⁻1 at pH 7, 30 °C. (kim2011divergenceofchemical pages 7-9)
• Metal activation benchmark: 3 mM Zn2+ → ~10-fold increase in initial velocity for metal-depleted enzyme in one mechanistic study. (kim2011divergenceofchemical pages 7-9)
• E. coli phn (C–P lyase) induction: ~100-fold under phosphate limitation; PhoB/PhoR dependent (Metcalf & Wanner, 1991-01, Journal of Bacteriology). (metcalf1991involvementofthe pages 11-11)

9) Evidence-backed conclusions for yjdM/P0AFJ1 in E. coli K-12

1. Identity: E. coli yjdM is explicitly stated to be formerly called phnA in E. coli literature, supporting correct gene mapping. (smithfrieday2022deletionofprou pages 5-8)
2. Biochemical function: Purified E. coli YjdM has phosphonoacetate hydrolase activity in vitro with substantial specific activity. (kim2023functionalannotationof pages 6-7, kim2023functionalannotationof media 4546f8e8)
3. Mechanistic class (context): Phosphonoacetate hydrolases characterized in other bacteria are alkaline phosphatase superfamily metalloenzymes with a Thr nucleophile and binuclear metal center; these studies provide mechanistic expectations but do not by themselves prove the identical active-site architecture in E. coli YjdM. (agarwal2011structuralandmechanistic pages 6-8, kim2011divergenceofchemical pages 1-2, kamat2013theenzymaticconversion pages 2-4)
4. Pathway role in E. coli: The canonical E. coli phosphonate utilization pathway is the Pho-regulated C–P lyase operon (phnCDEFGHIJLKMNOP). Foundational genetics indicates phnC–phnP are sufficient/required for phosphonate use, suggesting yjdM/phnA is not essential for the canonical phenotype. Therefore, the in vivo physiological role of YjdM remains unresolved. (metcalf1991involvementofthe pages 11-11, ruffolo2023themicrobialdegradation pages 8-10, crecylagard2025limitationsofcurrent pages 7-9)

Supporting figure

The following figure panel from Kim et al. (2023) provides direct visual evidence of the reported phosphonoacetate hydrolase specific activity for E. coli YjdM. (kim2023functionalannotationof media 4546f8e8)

Table: This table compacts the main functional-annotation evidence for E. coli K-12 yjdM/P0AFJ1, separating direct in vitro evidence in E. coli from mechanistic inference based on characterized PhnA homologs. It is useful for distinguishing what is experimentally established versus inferred for reaction, pathway placement, regulation, and localization.

References

1. (smithfrieday2022deletionofprou pages 5-8): Michelle N. Smith-Frieday, Craig H. Kerr, and Janet M. Wood. Deletion of prou suppresses proq phenotypes in escherichia coli. bioRxiv, Mar 2022. URL: https://doi.org/10.1101/2022.03.01.481631, doi:10.1101/2022.03.01.481631. This article has 1 citations.

2. (ruffolo2023themicrobialdegradation pages 8-10): Francesca Ruffolo, Tamara Dinhof, Leanne Murray, Erika Zangelmi, Jason P. Chin, Katharina Pallitsch, and Alessio Peracchi. The microbial degradation of natural and anthropogenic phosphonates. Molecules, 28:6863, Sep 2023. URL: https://doi.org/10.3390/molecules28196863, doi:10.3390/molecules28196863. This article has 37 citations.

3. (kim2023functionalannotationof pages 6-7): Gi Bae Kim, Ji Yeon Kim, Jong An Lee, Charles J. Norsigian, Bernhard O. Palsson, and Sang Yup Lee. Functional annotation of enzyme-encoding genes using deep learning with transformer layers. Nature Communications, Nov 2023. URL: https://doi.org/10.1038/s41467-023-43216-z, doi:10.1038/s41467-023-43216-z. This article has 110 citations and is from a highest quality peer-reviewed journal.

4. (kim2023functionalannotationof media 4546f8e8): Gi Bae Kim, Ji Yeon Kim, Jong An Lee, Charles J. Norsigian, Bernhard O. Palsson, and Sang Yup Lee. Functional annotation of enzyme-encoding genes using deep learning with transformer layers. Nature Communications, Nov 2023. URL: https://doi.org/10.1038/s41467-023-43216-z, doi:10.1038/s41467-023-43216-z. This article has 110 citations and is from a highest quality peer-reviewed journal.

5. (crecylagard2025limitationsofcurrent pages 7-9): Valérie de Crécy-Lagard, Raquel Dias, Nick Sexson, Iddo Friedberg, Yifeng Yuan, and Manal A. Swairjo. Limitations of current machine-learning models in predicting enzymatic functions for uncharacterized proteins. BioRxiv, Jul 2025. URL: https://doi.org/10.1101/2024.07.01.601547, doi:10.1101/2024.07.01.601547. This article has 8 citations.

6. (ruffolo2023themicrobialdegradation pages 2-4): Francesca Ruffolo, Tamara Dinhof, Leanne Murray, Erika Zangelmi, Jason P. Chin, Katharina Pallitsch, and Alessio Peracchi. The microbial degradation of natural and anthropogenic phosphonates. Molecules, 28:6863, Sep 2023. URL: https://doi.org/10.3390/molecules28196863, doi:10.3390/molecules28196863. This article has 37 citations.

7. (agarwal2011structuralandmechanistic pages 1-2): Vinayak Agarwal, Svetlana A. Borisova, William W. Metcalf, Wilfred A. van der Donk, and Satish K. Nair. Structural and mechanistic insights into c-p bond hydrolysis by phosphonoacetate hydrolase. Chemistry & Biology, 18(10):1230-1240, Oct 2011. URL: https://doi.org/10.1016/j.chembiol.2011.07.019, doi:10.1016/j.chembiol.2011.07.019. This article has 61 citations.

8. (kamat2013theenzymaticconversion pages 2-4): Siddhesh S Kamat and Frank M Raushel. The enzymatic conversion of phosphonates to phosphate by bacteria. Current opinion in chemical biology, 17 4:589-96, Aug 2013. URL: https://doi.org/10.1016/j.cbpa.2013.06.006, doi:10.1016/j.cbpa.2013.06.006. This article has 98 citations and is from a peer-reviewed journal.

9. (peck2013phosphonatebiosynthesisand pages 6-7): Spencer C Peck and Wilfred A van der Donk. Phosphonate biosynthesis and catabolism: a treasure trove of unusual enzymology. Current opinion in chemical biology, 17 4:580-8, Aug 2013. URL: https://doi.org/10.1016/j.cbpa.2013.06.018, doi:10.1016/j.cbpa.2013.06.018. This article has 80 citations and is from a peer-reviewed journal.

10. (agarwal2011structuralandmechanistic pages 4-5): Vinayak Agarwal, Svetlana A. Borisova, William W. Metcalf, Wilfred A. van der Donk, and Satish K. Nair. Structural and mechanistic insights into c-p bond hydrolysis by phosphonoacetate hydrolase. Chemistry & Biology, 18(10):1230-1240, Oct 2011. URL: https://doi.org/10.1016/j.chembiol.2011.07.019, doi:10.1016/j.chembiol.2011.07.019. This article has 61 citations.

11. (kim2011divergenceofchemical pages 7-9): Alexander Kim, Matthew M. Benning, Sang OkLee, John Quinn, Brian M. Martin, Hazel M. Holden, and Debra Dunaway-Mariano. Divergence of chemical function in the alkaline phosphatase superfamily: structure and mechanism of the p-c bond cleaving enzyme phosphonoacetate hydrolase. Biochemistry, 50 17:3481-94, May 2011. URL: https://doi.org/10.1021/bi200165h, doi:10.1021/bi200165h. This article has 38 citations and is from a peer-reviewed journal.

12. (kim2011divergenceofchemical pages 1-2): Alexander Kim, Matthew M. Benning, Sang OkLee, John Quinn, Brian M. Martin, Hazel M. Holden, and Debra Dunaway-Mariano. Divergence of chemical function in the alkaline phosphatase superfamily: structure and mechanism of the p-c bond cleaving enzyme phosphonoacetate hydrolase. Biochemistry, 50 17:3481-94, May 2011. URL: https://doi.org/10.1021/bi200165h, doi:10.1021/bi200165h. This article has 38 citations and is from a peer-reviewed journal.

13. (agarwal2011structuralandmechanistic pages 6-8): Vinayak Agarwal, Svetlana A. Borisova, William W. Metcalf, Wilfred A. van der Donk, and Satish K. Nair. Structural and mechanistic insights into c-p bond hydrolysis by phosphonoacetate hydrolase. Chemistry & Biology, 18(10):1230-1240, Oct 2011. URL: https://doi.org/10.1016/j.chembiol.2011.07.019, doi:10.1016/j.chembiol.2011.07.019. This article has 61 citations.

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