ReviewThe Journal of biological chemistry2012
Divergence and convergence in enzyme evolution.
Review in The Journal of biological chemistry, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 88 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
88 citing papers in PubMed, 167 citations in OpenAlex.
- Article
- Secreted retropepsin-like enzymes are essential for stress tolerance and biofilm formation inmBio · 2025Article
- Paradigms of convergent evolution in enzymes.The FEBS journal · 2025Article
- Optimizing Ligand Valency to Maximize Tendon Accumulation of Peptide-Targeted Nanoparticles.ACS applied materials & interfaces · 2024Article
- Effect of berry maturity stages on the germination and protein constituents of African nightshade (Solanum scabrum) seeds.Scientific reports · 2024Article
- Crystal Lattice-Induced Stress modulates Photoinduced Jahn-Teller Distortion Dynamics.ACS physical chemistry Au · 2024Article
- Re-appraising the evidence for the source, regulation and function of p53-family isoforms.Nucleic acids research · 2024Review
- Protein Fold Usages in Ribosomes: Another Glance to the Past.International journal of molecular sciences · 2024Article
- New bacterial strains for ibuprofen biodegradation: Drug removal, transformation, and potential catabolic genes.Environmental microbiology reports · 2024Article
- Gut microbiota DPP4-like enzymes are increased in type-2 diabetes and contribute to incretin inactivation.Genome biology · 2024Article
- Biosynthesis and function of 7-deazaguanine derivatives in bacteria and phages.Microbiology and molecular biology reviews : MMBR · 2024Review
- Phylogenetic Analysis Guides Transporter Protein Deorphanization: A Case Study of the SLC25 Family of Mitochondrial Metabolite Transporters.Biomolecules · 2023Article
- Capturing the geometry, function, and evolution of enzymes with 3D templates.Protein science : a publication of the Protein Society · 2022Review
- Sequence Conservation, Domain Architectures, and Phylogenetic Distribution of the HD-GYP Type c-di-GMP Phosphodiesterases.Journal of bacteriology · 2022Review
- Conformational Variation in Enzyme Catalysis: A Structural Study on Catalytic Residues.Journal of molecular biology · 2022Article
- Free-Energy Profile Analysis of the Catalytic Reaction of Glycinamide Ribonucleotide Synthetase.Life (Basel, Switzerland) · 2022Article
- Structural dynamics in the evolution of a bilobed protein scaffold.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- β-Barrels and Amyloids: Structural Transitions, Biological Functions, and Pathogenesis.International journal of molecular sciences · 2021Review
- Article
- Review
28 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Comparative analysis of the sequences of enzymes encoded in a variety of prokaryotic and eukaryotic genomes reveals convergence and divergence at several levels. Functional convergence can be inferred when structurally distinct and hence non-homologous enzymes show the ability to catalyze the same biochemical reaction. In contrast, as a result of functional diversification, many structurally similar enzyme molecules act on substantially distinct substrates and catalyze diverse biochemical reactions. Here, we present updates on the ATP-grasp, alkaline phosphatase, cupin, HD hydrolase, and N-terminal nucleophile (Ntn) hydrolase enzyme superfamilies and discuss the patterns of sequence and structural conservation and diversity within these superfamilies. Typically, enzymes within a superfamily possess common sequence motifs and key active site residues, as well as (predicted) reaction mechanisms. These observations suggest that the strained conformation (the entatic state) of the active site, which is responsible for the substrate binding and formation of the transition complex, tends to be conserved within enzyme superfamilies. The subsequent fate of the transition complex is not necessarily conserved and depends on the details of the structures of the enzyme and the substrate. This variability of reaction outcomes limits the ability of sequence analysis to predict the exact enzymatic activities of newly sequenced gene products. Nevertheless, sequence-based (super)family assignments and generic functional predictions, even if imprecise, provide valuable leads for experimental studies and remain the best approach to the functional annotation of uncharacterized proteins from new genomes.
Indexed as
Identifiers
What OpenQuestion holds
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.