ArticleProceedings of the National Academy of Sciences of the United States of America2013
Consequences of domain insertion on sequence-structure divergence in a superfold.
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 18 papers.
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Who cites it
18 citing papers in PubMed.
- Family-level specialization in protein domain insertion architectures.Protein science : a publication of the Protein Society · 2026Article
- A SARS-CoV-2 Vaccine Designed for Manufacturability Results in Unexpected Potency and Non-Waning Humoral Response.Vaccines · 2023Article
- General strategies for using amino acid sequence data to guide biochemical investigation of protein function.Biochemical Society transactions · 2022Review
- Mechanisms of protein evolution.Protein science : a publication of the Protein Society · 2022Review
- Crystal structure of a lipin/Pah phosphatidic acid phosphatase.Nature communications · 2020Article
- Crystal structure of an assembly intermediate of respiratory Complex II.Nature communications · 2018Article
- Biology, Mechanism, and Structure of Enzymes in the α-d-Phosphohexomutase Superfamily.Advances in protein chemistry and structural biology · 2017Article
- Catalytic scaffolds for phosphoryl group transfer.Current opinion in structural biology · 2016Review
- Chopping and Changing: the Evolution of the Flavin-dependent Monooxygenases.Journal of molecular biology · 2016Article
- Article
- Precise assembly of complex beta sheet topologies from de novo designed building blocks.eLife · 2015Article
- Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks.Biochimica et biophysica acta · 2015Review
- Panoramic view of a superfamily of phosphatases through substrate profiling.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- In the multi-domain protein adenylate kinase, domain insertion facilitates cooperative folding while accommodating function at domain interfaces.PLoS computational biology · 2014Article
- New insights about enzyme evolution from large scale studies of sequence and structure relationships.The Journal of biological chemistry · 2014Review
- Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- The evolution of enzyme function in the isomerases.Current opinion in structural biology · 2014Review
- Chronophin dimerization is required for proper positioning of its substrate specificity loop.The Journal of biological chemistry · 2014Article
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Authors and funding
8 authors.
Funding
Abstract
Although the universe of protein structures is vast, these innumerable structures can be categorized into a finite number of folds. New functions commonly evolve by elaboration of existing scaffolds, for example, via domain insertions. Thus, understanding structural diversity of a protein fold evolving via domain insertions is a fundamental challenge. The haloalkanoic dehalogenase superfamily serves as an excellent model system wherein a variable cap domain accessorizes the ubiquitous Rossmann-fold core domain. Here, we determine the impact of the cap-domain insertion on the sequence and structure divergence of the core domain. Through quantitative analysis on a unique dataset of 154 core-domain-only and cap-domain-only structures, basic principles of their evolution have been uncovered. The relationship between sequence and structure divergence of the core domain is shown to be monotonic and independent of the corresponding type of domain insert, reflecting the robustness of the Rossmann fold to mutation. However, core domains with the same cap type share greater similarity at the sequence and structure levels, suggesting interplay between the cap and core domains. Notably, results reveal that the variance in structure maps to α-helices flanking the central β-sheet and not to the domain-domain interface. Collectively, these results hint at intramolecular coevolution where the fold diverges differentially in the context of an accessory domain, a feature that might also apply to other multidomain superfamilies.
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