ArticlePloS one2013
Protein similarity networks reveal relationships among sequence, structure, and function within the Cupin superfamily.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 65 citations in OpenAlex.
- Article
- Paleoproteomics of pottery food residues reveals plant cupin superfamily proteins preserved for thousands of years.iScience · 2026Article
- Disordered N-termini enhance the thermostability of SGNH-hydrolase family polyesterases.Protein science : a publication of the Protein Society · 2026Article
- Thermostable Bacterial Esterases From Lipase Family 1.5 Degrade Compostable Polyesters PBAT and PBSA.MicrobiologyOpen · 2025Article
- Structural insights into the enzymatic breakdown of azomycin-derived antibiotics by 2-nitroimdazole hydrolase (NnhA).Communications biology · 2024Article
- Substrate Specificities of Variants of Barley (1,3)- and (1,3;1,4)-β-d-Glucanases Resulting from Mutagenesis and Segment Hybridization.Biochemistry · 2024Article
- An oxalate decarboxylase-like cupin domain containing protein is involved in imparting acid stress tolerance in Bacillus amyloliquefaciens MBNC.World journal of microbiology & biotechnology · 2024Article
- Differences in the Second Coordination Sphere Tailor the Substrate Specificity and Reactivity of Thiol Dioxygenases.Accounts of chemical research · 2022Article
- FoCupin1, a Cupin_1 domain-containing protein, is necessary for the virulence ofFrontiers in microbiology · 2022Article
- Characterization of a Secretory YML079-like Cupin Protein That Contributes toMicroorganisms · 2021Article
- Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts.Viruses · 2021Article
- The metal- and substrate-dependences of 2,4'-dihydroxyacetophenone dioxygenase.Archives of biochemistry and biophysics · 2020Article
- The 3-His Metal Coordination Site Promotes the Coupling of Oxygen Activation to Cysteine Oxidation in Cysteine Dioxygenase.Biochemistry · 2020Article
- Rv1717 Is a Cell Wall - Associated β-Galactosidase ofFrontiers in microbiology · 2020Article
- Illuminating the catalytic core of ectoine synthase through structural and biochemical analysis.Scientific reports · 2019Article
- Revisiting the methionine salvage pathway and its paralogues.Microbial biotechnology · 2019Article
- A global view of structure-function relationships in the tautomerase superfamily.The Journal of biological chemistry · 2018Article
- Yield Improvement of the Anti-MRSA Antibiotics WAP-8294A by CRISPR/dCas9 Combined with Refactoring Self-Protection Genes in Lysobacter enzymogenes OH11.ACS synthetic biology · 2018Article
- Ectopic RING zinc finger gene from hot pepper induces totally different genes in lettuce and tobacco.Molecular breeding : new strategies in plant improvement · 2018Article
- Pac13 is a Small, Monomeric Dehydratase that Mediates the Formation of the 3'-Deoxy Nucleoside of Pacidamycins.Angewandte Chemie (International ed. in English) · 2017Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The cupin superfamily is extremely diverse and includes catalytically inactive seed storage proteins, sugar-binding metal-independent epimerases, and metal-dependent enzymes possessing dioxygenase, decarboxylase, and other activities. Although numerous proteins of this superfamily have been structurally characterized, the functions of many of them have not been experimentally determined. We report the first use of protein similarity networks (PSNs) to visualize trends of sequence and structure in order to make functional inferences in this remarkably diverse superfamily. PSNs provide a way to visualize relatedness of structure and sequence among a given set of proteins. Structure- and sequence-based clustering of cupin members reflects functional clustering. Networks based only on cupin domains and networks based on the whole proteins provide complementary information. Domain-clustering supports phylogenetic conclusions that the N- and C-terminal domains of bicupin proteins evolved independently. Interestingly, although many functionally similar enzymatic cupin members bind the same active site metal ion, the structure and sequence clustering does not correlate with the identity of the bound metal. It is anticipated that the application of PSNs to this superfamily will inform experimental work and influence the functional annotation of databases.
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