ArticleProceedings of the National Academy of Sciences of the United States of America2013
Prediction and experimental validation of enzyme substrate specificity in protein structures.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Bridging Algorithms and Biocatalysis: Perspectives on AI-Supported Enzyme Engineering.Molecules (Basel, Switzerland) · 2026Review
- Antimicrobial activity of compounds identified by artificial intelligence discovery engine targeting enzymes involved in Neisseria gonorrhoeae peptidoglycan metabolism.Biological research · 2024Article
- Machine Learning to Predict Enzyme-Substrate Interactions in Elucidation of Synthesis Pathways: A Review.Metabolites · 2024Review
- Identification of evolutionarily stable functional and immunogenic sites across the SARS-CoV-2 proteome and greater coronavirus family.Bioinformatics (Oxford, England) · 2021Article
- Uncovering DNA-PKcs ancient phylogeny, unique sequence motifs and insights for human disease.Progress in biophysics and molecular biology · 2021Article
- Identification of evolutionarily stable functional and immunogenic sites across the SARS-CoV-2 proteome and the greater coronavirus family.Research square · 2021Article
- Biochemical Characterization of ArylamineFrontiers in microbiology · 2020Article
- Evolutionary Stability of Salt Bridges Hints Its Contribution to Stability of Proteins.Computational and structural biotechnology journal · 2019Article
- Automated shape-based clustering of 3D immunoglobulin protein structures in chronic lymphocytic leukemia.BMC bioinformatics · 2018Article
- Point mutation Arg153-His at surface of Bacillus lipase contributing towards increased thermostability and ester synthesis: insight into molecular network.Molecular and cellular biochemistry · 2018Article
- Objective assessment of the evolutionary action equation for the fitness effect of missense mutations across CAGI-blinded contests.Human mutation · 2017Review
- UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures.Nucleic acids research · 2016Article
- Template-based prediction of protein function.Current opinion in structural biology · 2015Review
- Evolutionary Action Score of TP53 Identifies High-Risk Mutations Associated with Decreased Survival and Increased Distant Metastases in Head and Neck Cancer.Cancer research · 2015Article
- DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe.BMC bioinformatics · 2015Article
- Genetically modified proteins: functional improvement and chimeragenesis.Bioengineered · 2015Review
- A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness.Genome research · 2014Article
- Determining microbial products and identifying molecular targets in the human microbiome.Cell metabolism · 2014Review
- Leveraging structure for enzyme function prediction: methods, opportunities, and challenges.Trends in biochemical sciences · 2014Review
- Prediction and redesign of protein-protein interactions.Progress in biophysics and molecular biologyReview
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Authors and funding
5 authors.
Funding
Abstract
Structural Genomics aims to elucidate protein structures to identify their functions. Unfortunately, the variation of just a few residues can be enough to alter activity or binding specificity and limit the functional resolution of annotations based on sequence and structure; in enzymes, substrates are especially difficult to predict. Here, large-scale controls and direct experiments show that the local similarity of five or six residues selected because they are evolutionarily important and on the protein surface can suffice to identify an enzyme activity and substrate. A motif of five residues predicted that a previously uncharacterized Silicibacter sp. protein was a carboxylesterase for short fatty acyl chains, similar to hormone-sensitive-lipase-like proteins that share less than 20% sequence identity. Assays and directed mutations confirmed this activity and showed that the motif was essential for catalysis and substrate specificity. We conclude that evolutionary and structural information may be combined on a Structural Genomics scale to create motifs of mixed catalytic and noncatalytic residues that identify enzyme activity and substrate specificity.
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