ArticleThe Journal of biological chemistry2020
Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenic
Article in The Journal of biological chemistry, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 48 citations in OpenAlex.
- Genome mining of Trp-anthranilic acid cyclic dipeptides in Aspergillus driven by analysis of NRPS adenylation domains.Archives of microbiology · 2026Article
- Structural Determinants of Catalytic Bias in an AMP-Forming Acetyl-CoA Synthetase frombioRxiv : the preprint server for biology · 2026Article
- PARAS: High-Accuracy Machine Learning of Substrate Specificities in Nonribosomal Peptide Synthetases.JACS Au · 2026Article
- Model-driven exploration of lactose and galactose metabolism via an oxidoreductive pathway in Sungouiella intermedia for cell factory applications.Microbial cell factories · 2026Article
- Diversity of FAAL enzymes and prediction of their substrate specificity using FAALPred.Protein science : a publication of the Protein Society · 2026Article
- Machine learning for enzyme catalytic activity: current progress and future horizons.Briefings in bioinformatics · 2026Review
- Unlocking microbial potential: advances in omics and bioinformatics for aromatic hydrocarbon degradation.World journal of microbiology & biotechnology · 2025Review
- Enzymatic carbon-fluorine bond cleavage by human gut microbes.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Dual feedback inhibition of ATP-dependent caffeate activation economizes ATP in caffeate-dependent electron bifurcation.Applied and environmental microbiology · 2024Article
- RAIChU: automating the visualisation of natural product biosynthesis.Journal of cheminformatics · 2024Article
- Structural, biochemical and bioinformatic analyses of nonribosomal peptide synthetase adenylation domains.Natural product reports · 2024Review
- Acetyl-CoA synthetase activity is enzymatically regulated by lysine acetylation using acetyl-CoA or acetyl-phosphate as donor molecule.Nature communications · 2024Article
- PEARL-Catalyzed Peptide Bond Formation after Chain Reversal by Ureido-Forming Condensation Domains.ACS central science · 2024Article
- Article
- Chemical structure metagenomics of microbial natural products: surveying nonribosomal peptides and beyond.Beilstein journal of organic chemistry · 2024Article
- Repurposing conformational changes in ANL superfamily enzymes to rapidly generate biosensors for organic and amino acids.Nature communications · 2023Article
- Incorporation and modification of fatty acids in cyanobacterial natural products biosynthesis.Chemical communications (Cambridge, England) · 2023Review
- The benzoyl-CoA pathway serves as a genomic marker to identify the oxygen requirements in the degradation of aromatic hydrocarbons.Frontiers in microbiology · 2023Article
- Review
- Enzymatic assembly of the salinosporamide γ-lactam-β-lactone anticancer warhead.Nature chemical biology · 2022Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Enzymes that cleave ATP to activate carboxylic acids play essential roles in primary and secondary metabolism in all domains of life. Class I adenylate-forming enzymes share a conserved structural fold but act on a wide range of substrates to catalyze reactions involved in bioluminescence, nonribosomal peptide biosynthesis, fatty acid activation, and β-lactone formation. Despite their metabolic importance, the substrates and functions of the vast majority of adenylate-forming enzymes are unknown without tools available to accurately predict them. Given the crucial roles of adenylate-forming enzymes in biosynthesis, this also severely limits our ability to predict natural product structures from biosynthetic gene clusters. Here we used machine learning to predict adenylate-forming enzyme function and substrate specificity from protein sequences. We built a web-based predictive tool and used it to comprehensively map the biochemical diversity of adenylate-forming enzymes across >50,000 candidate biosynthetic gene clusters in bacterial, fungal, and plant genomes. Ancestral phylogenetic reconstruction and sequence similarity networking of enzymes from these clusters suggested divergent evolution of the adenylate-forming superfamily from a core enzyme scaffold most related to contemporary CoA ligases toward more specialized functions including β-lactone synthetases. Our classifier predicted β-lactone synthetases in uncharacterized biosynthetic gene clusters conserved in >90 different strains of
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.