ArticleThe Journal of biological chemistry2010
Circular permutation provides an evolutionary link between two families of calcium-dependent carbohydrate binding modules.
Article in The Journal of biological chemistry, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 61 citations in OpenAlex.
- Systematic discovery of circular permutations across the protein universe using CIRPIN.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- CIRPIN: Learning Circular Permutation-Invariant Representations to Uncover Putative Protein Homologs.bioRxiv : the preprint server for biology · 2025Article
- Evolutionary model of repeat insertions in Ataxin-3 traces the origin of the polyglutamine stretch to an ancestral ubiquitin binding module.Protein science : a publication of the Protein Society · 2024Article
- Unique Fn3-like biosensor in σProtein science : a publication of the Protein Society · 2024Article
- Structural and biochemical insight into a modular β-1,4-galactan synthase in plants.Nature plants · 2023Article
- Inhibitory effect of lignin on the hydrolysis of xylan by thermophilic and thermolabile GH11 xylanases.Biotechnology for biofuels and bioproducts · 2022Article
- A bioactive ligand-conjugated iridium(III) metal-based complex as a Keap1-Nrf2 protein-protein interaction inhibitor against acetaminophen-induced acute liver injury.Redox biology · 2021Article
- Proteome-wide prediction of bacterial carbohydrate-binding proteins as a tool for understanding commensal and pathogen colonisation of the vaginal microbiome.NPJ biofilms and microbiomes · 2021Article
- In silico screening and experimental analysis of family GH11 xylanases for applications under conditions of alkaline pH and high temperature.Biotechnology for biofuels · 2020Article
- Carbohydrate Binding Modules: Diversity of Domain Architecture in Amylases and Cellulases From Filamentous Microorganisms.Frontiers in bioengineering and biotechnology · 2020Review
- Article
- Insights into the mechanism(s) of digestion of crystalline cellulose by plant class C GH9 endoglucanases.Journal of molecular modeling · 2019Article
- Mathematical Basis of Predicting Dominant Function in Protein Sequences by a Generic HMM-ANN Algorithm.Acta biotheoretica · 2018Article
- Origin, evolution, and divergence of plant class C GH9 endoglucanases.BMC evolutionary biology · 2018Article
- Structural and functional analysis of de-N-acetylase PgaB from periodontopathogen Aggregatibacter actinomycetemcomitans.Molecular oral microbiology · 2017Article
- Identification of a novel family of carbohydrate-binding modules with broad ligand specificity.Scientific reports · 2016Article
- In silico Identification and Taxonomic Distribution of Plant Class C GH9 Endoglucanases.Frontiers in plant science · 2016Article
- Convergent and divergent mechanisms of sugar recognition across kingdoms.Current opinion in structural biology · 2014Review
- The structure of a Streptomyces avermitilis α-L-rhamnosidase reveals a novel carbohydrate-binding module CBM67 within the six-domain arrangement.The Journal of biological chemistry · 2013Article
- How nature can exploit nonspecific catalytic and carbohydrate binding modules to create enzymatic specificity.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
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Authors and funding
13 authors at 4 institutions in 3 countries.
Funding
Abstract
The microbial deconstruction of the plant cell wall is a critical biological process, which also provides important substrates for environmentally sustainable industries. Enzymes that hydrolyze the plant cell wall generally contain non-catalytic carbohydrate binding modules (CBMs) that contribute to plant cell wall degradation. Here we report the biochemical properties and crystal structure of a family of CBMs (CBM60) that are located in xylanases. Uniquely, the proteins display broad ligand specificity, targeting xylans, galactans, and cellulose. Some of the CBM60s display enhanced affinity for their ligands through avidity effects mediated by protein dimerization. The crystal structure of vCBM60, displays a β-sandwich with the ligand binding site comprising a broad cleft formed by the loops connecting the two β-sheets. Ligand recognition at site 1 is, exclusively, through hydrophobic interactions, whereas binding at site 2 is conferred by polar interactions between a protein-bound calcium and the O2 and O3 of the sugar. The observation, that ligand recognition at site 2 requires only a β-linked sugar that contains equatorial hydroxyls at C2 and C3, explains the broad ligand specificity displayed by vCBM60. The ligand-binding apparatus of vCBM60 displays remarkable structural conservation with a family 36 CBM (CBM36); however, the residues that contribute to carbohydrate recognition are derived from different regions of the two proteins. Three-dimensional structure-based sequence alignments reveal that CBM36 and CBM60 are related by circular permutation. The biological and evolutionary significance of the mechanism of ligand recognition displayed by family 60 CBMs is discussed.
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