Using structure to inform carbohydrate binding module function

Abbott, D. Wade; Bueren, A. Lammerts van

doi:10.1016/j.sbi.2014.07.004

Cited by 92 publications

(70 citation statements)

References 55 publications

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“…2b). These molecular determinants of starch recognition are shared with most starch-binding CBMs [45, 46], as well as the surface starch-binding sites of some GH13 enzymes [47, 48]. Thus, the glycan-binding site of SusD may be an example of convergent evolution whereby proteins of distinct evolutionary lineage and hence structure evolve similar functions [49].…”

Section: Susd: An A-helical Carbohydrate-binding Proteinmentioning

confidence: 99%

The Sus operon: a model system for starch uptake by the human gut Bacteroidetes

Foley

Cockburn

Koropatkin

2016

Cell. Mol. Life Sci.

200

157

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Resident bacteria in the densely populated human intestinal tract must efficiently compete for carbohydrate nutrition. The Bacteroidetes, a dominant bacterial phylum in the mammalian gut, encode a plethora of discrete polysaccharide utilization loci (PULs) that are selectively activated to facilitate glycan capture at the cell surface. The most well-studied PUL-encoded glycan-up-take system is the starch utilization system (Sus) of Bacteroides thetaiotaomicron. The Sus includes the requisite proteins for binding and degrading starch at the surface of the cell preceding oligosaccharide transport across the outer membrane for further depolymerization to glucose in the periplasm. All mammalian gut Bacteroidetes possess analogous Sus-like systems that target numerous diverse glycans. In this review, we discuss what is known about the eight Sus proteins of B. thetaiotaomicron that define the Sus-like paradigm of nutrient acquisition that is exclusive to the Gram-negative Bacteroidetes. We emphasize the well-characterized outer membrane proteins SusDEF and the α-amylase SusG, each of which have unique structural features that allow them to interact with starch on the cell surface. Despite the apparent redundancy in starch-binding sites among these proteins, each has a distinct role during starch catabolism. Additionally, we consider what is known about how these proteins dynamically interact and cooperate in the membrane and propose a model for the formation of the Sus outer membrane complex.

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Section: Susd: An A-helical Carbohydrate-binding Proteinmentioning

confidence: 99%

The Sus operon: a model system for starch uptake by the human gut Bacteroidetes

Foley

Cockburn

Koropatkin

2016

Cell. Mol. Life Sci.

200

157

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“…the so-called "orphan CBMs," have been described (2). Based on amino acid sequence similarity, they are classified into different families (CAZy); currently 71 are known, and the number is still increasing (3).…”

Section: The Atomic Coordinates and Structure Factors (Codes 4xup 4xmentioning

confidence: 99%

Exploring Multimodularity in Plant Cell Wall Deconstruction

Sainz-Polo

González

Menéndez

et al. 2015

Journal of Biological Chemistry

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Background: Multimodularity is essential in most plant cell wall recycling enzymes. Results: The CBM22-1-CBM22-2 tandem possesses extraordinary plasticity and two sites with different affinities. CBM22-2 exhibits novel specificity within CBM22s. Conclusion: Depolymerization of highly substituted arabinoxylans by Xyn10C and a delivery strategy mediated by Xyn10C-XBD are proposed. Significance: Elucidating the mechanisms regulating specificity through multimodularity is crucial for producing efficient biocatalysts for biomass deconstruction.

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“…Context encompasses such properties as the overall structure of the glycan, the nature of the underlying aglycone (protein, lipid, etc), glycan clustering (avidity), the presentation of the glycan relative to its environment [21], the specificity of modules attached to nonspecific catalytic domains [22,23] and the composition of the cellular membrane [24]. …”

Section: Introductionmentioning

confidence: 99%

Recent advances in employing molecular modelling to determine the specificity of glycan-binding proteins

Grant

Woods

2014

Current Opinion in Structural Biology

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Impressive improvements in docking performance can be achieved by applying energy bonuses to poses in which glycan hydroxyl groups occupy positions otherwise preferred by bound waters. In addition, inclusion of glycosidic conformational energies allows unlikely glycan conformations to be appropriately penalized. A method for predicting the binding specificity of glycan-binding proteins has been developed, which is based on grafting glycan branches onto a minimal binding determinant in the binding site. Grafting can be used either to screen virtual libraries of glycans, such as the known glycome, or to identify docked poses of minimal binding determinants that are consistent with specificity data. The reviewed advances allow accurate modelling of carbohydrate-protein 3D co-complexes, but challenges remain in ranking the affinity of congeners.

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Using structure to inform carbohydrate binding module function

Cited by 92 publications

References 55 publications

The Sus operon: a model system for starch uptake by the human gut Bacteroidetes

The Sus operon: a model system for starch uptake by the human gut Bacteroidetes

Exploring Multimodularity in Plant Cell Wall Deconstruction

Recent advances in employing molecular modelling to determine the specificity of glycan-binding proteins

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