ArticleNature2007
Structure-based activity prediction for an enzyme of unknown function.
Article in Nature, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 127 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
127 citing papers in PubMed.
- Exploring neural networks to uncover information-richer features for protein interaction prediction.European biophysics journal : EBJ · 2026Article
- On the Origin of Substrate Specificity of Enzymes from the Amidohydrolase Superfamily.Angewandte Chemie (International ed. in English) · 2026Article
- Biological evaluation and molecular docking studies of novel aza-acyclic nucleosides as putative antimicrobial, anticancer, and antioxidant agents.BMC chemistry · 2025Article
- Predicting Protein Function in the AI and Big Data Era.Biochemistry · 2025Review
- Compact Assessment of Molecular Surface Complementarities Enhances Neural Network-Aided Prediction of Key Binding Residues.Journal of chemical information and modeling · 2025Article
- A Practical Guide to Computational Tools for Engineering Biocatalytic Properties.International journal of molecular sciences · 2025Review
- Structure, function and substrate preferences of archaeal S-adenosyl-L-homocysteine hydrolases.Communications biology · 2024Article
- DeepProSite: structure-aware protein binding site prediction using ESMFold and pretrained language model.Bioinformatics (Oxford, England) · 2023Article
- Synthesis of Metabolites and Metabolite-like Compounds Using Biocatalytic Systems.Metabolites · 2023Review
- Cell-Effective Transition-State Analogue of PhenylethanolamineBiochemistry · 2023Article
- Total enzymatic synthesis of cis-α-irone from a simple carbon source.Nature communications · 2022Article
- Activity-based annotation: the emergence of systems biochemistry.Trends in biochemical sciences · 2022Review
- Article
- RadicalSAM.org: A Resource to Interpret Sequence-Function Space and Discover New Radical SAM Enzyme Chemistry.ACS bio & med chem Au · 2022Article
- FRAGSITE: A Fragment-Based Approach for Virtual Ligand Screening.Journal of chemical information and modeling · 2021Article
- 2D Zernike polynomial expansion: Finding the protein-protein binding regions.Computational and structural biotechnology journal · 2021Article
- Transition-State Analogues of PhenylethanolamineJournal of the American Chemical Society · 2020Article
- Chemometric Models of Differential Amino Acids at the NaMolecules (Basel, Switzerland) · 2020Article
- Article
- Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning.Nature methods · 2020Article
67 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
Abstract
With many genomes sequenced, a pressing challenge in biology is predicting the function of the proteins that the genes encode. When proteins are unrelated to others of known activity, bioinformatics inference for function becomes problematic. It would thus be useful to interrogate protein structures for function directly. Here, we predict the function of an enzyme of unknown activity, Tm0936 from Thermotoga maritima, by docking high-energy intermediate forms of thousands of candidate metabolites. The docking hit list was dominated by adenine analogues, which appeared to undergo C6-deamination. Four of these, including 5-methylthioadenosine and S-adenosylhomocysteine (SAH), were tested as substrates, and three had substantial catalytic rate constants (10(5) M(-1 )s(-1)). The X-ray crystal structure of the complex between Tm0936 and the product resulting from the deamination of SAH, S-inosylhomocysteine, was determined, and it corresponded closely to the predicted structure. The deaminated products can be further metabolized by T. maritima in a previously uncharacterized SAH degradation pathway. Structure-based docking with high-energy forms of potential substrates may be a useful tool to annotate enzymes for function.
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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.