ArticlePLoS biology2016
An Ancient Fingerprint Indicates the Common Ancestry of Rossmann-Fold Enzymes Utilizing Different Ribose-Based Cofactors.
Article in PLoS biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 54 papers.
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54 citing papers in PubMed.
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- Physics Determines and Evolution Shapes Basic Units of Protein Function and Allosteric Regulation.Methods in molecular biology (Clifton, N.J.) · 2026Review
- Coenzyme-protein interactions since early life.eLife · 2025Article
- On the emergence of metabolism: the evolution of proteins that powered life.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2025Review
- Distribution of Polyphosphate Kinase 2 Genes in Bacteria Underscores a Dynamic Evolutionary History.Proteins · 2025Article
- Redefining the Limits of Functional Continuity in the Early Evolution of P-Loop NTPases.Molecular biology and evolution · 2025Article
- Bioinformatics study of biotin carboxylase B-subdomain isolated fromBiotechnologia · 2025Article
- Order of amino acid recruitment into the genetic code resolved by last universal common ancestor's protein domains.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Order of amino acid recruitment into the genetic code resolved by Last Universal Common Ancestor's protein domains.bioRxiv : the preprint server for biology · 2024Article
- Protein Fold Usages in Ribosomes: Another Glance to the Past.International journal of molecular sciences · 2024Article
- Methyl transfer in psilocybin biosynthesis.Nature communications · 2024Article
- Back in time to the Gly-rich prototype of the phosphate binding elementary function.Current research in structural biology · 2024Review
- Revealing Drivers for Carboxy-ACS chemical biology · 2023Article
- Biological Catalysis and Information Storage Have Relied onBiomolecules · 2023Review
- On the Origins of Enzymes: Phosphate-Binding Polypeptides Mediate Phosphoryl Transfer to Synthesize Adenosine Triphosphate.Journal of the American Chemical Society · 2023Article
- Why we are made of proteins and nucleic acids: Structural biology views on extraterrestrial life.Biophysics and physicobiology · 2023Article
- Structural similarities between SAM and ATP recognition motifs and detection of ATP binding in a SAM binding DNA methyltransferase.Current research in structural biology · 2023Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Nucleoside-based cofactors are presumed to have preceded proteins. The Rossmann fold is one of the most ancient and functionally diverse protein folds, and most Rossmann enzymes utilize nucleoside-based cofactors. We analyzed an omnipresent Rossmann ribose-binding interaction: a carboxylate side chain at the tip of the second β-strand (β2-Asp/Glu). We identified a canonical motif, defined by the β2-topology and unique geometry. The latter relates to the interaction being bidentate (both ribose hydroxyls interacting with the carboxylate oxygens), to the angle between the carboxylate and the ribose, and to the ribose's ring configuration. We found that this canonical motif exhibits hallmarks of divergence rather than convergence. It is uniquely found in Rossmann enzymes that use different cofactors, primarily SAM (S-adenosyl methionine), NAD (nicotinamide adenine dinucleotide), and FAD (flavin adenine dinucleotide). Ribose-carboxylate bidentate interactions in other folds are not only rare but also have a different topology and geometry. We further show that the canonical geometry is not dictated by a physical constraint--geometries found in noncanonical interactions have similar calculated bond energies. Overall, these data indicate the divergence of several major Rossmann-fold enzyme classes, with different cofactors and catalytic chemistries, from a common pre-LUCA (last universal common ancestor) ancestor that possessed the β2-Asp/Glu motif.
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