Structure determination of a sugar-binding protein from the phytopathogenic bacterium Xanthomonas citri

Molecular analysis of cyclic α-maltosyl-(1→6)-maltose binding protein in the bacterial metabolic pathway

Cyclic α-maltosyl-(1→6)-maltose (CMM) is a cyclic glucotetrasaccharide with alternating α-1,4 and α-1,6 linkages. Here, we report functional and structural analyses on CMM-binding protein (CMMBP), which is a substrate-binding protein (SBP) of an ABC importer system of the bacteria Arthrobacter globiformis. Isothermal titration calorimetry analysis revealed that CMMBP specifically bound to CMM with a K_d value of 9.6 nM. The crystal structure of CMMBP was determined at a resolution of 1.47 Å, and a panose molecule was bound in a cleft between two domains. To delineate its structural features, the crystal structure of CMMBP was compared with other SBPs specific for carbohydrates, such as cyclic α-nigerosyl-(1→6)-nigerose and cyclodextrins. These results indicate that A. globiformis has a unique metabolic pathway specialized for CMM.

Conformational Trapping of a β-Glucosides-Binding Protein Unveils the Selective Two-Step Ligand-Binding Mechanism of ABC Importers

Substrate-binding proteins (SBPs), selectively capture ligand(s) and ensure their translocation via its cognate ATP-binding cassette (ABC) import system. SBPs bind their cognate ligand(s) via an induced-fit mechanism known as the "Venus Fly-trap"; however, this mechanism lacks the atomic details of all conformational landscape as the confirmatory evidence(s) in its support. In this study, we delineate the atomic details of an SBP, β-glucosides-binding protein (βGlyBP) from Thermus thermophilus HB8. The protein βGlyBP is multi-specific and binds to different types of β-glucosides varying in their glycosidic linkages viz. β-1,2; β-1,3; β-1,4 and β-1,6 with a degree of polymerization of 2-5 glucosyl units. Structurally, the protein βGlyBP possesses four subdomains (N1, N2, C1 and C2). The unliganded protein βGlyBP remains in an open state, which closes upon binding to sophorose (SOP2), laminari-oligosaccharides (LAMn), cello-oligosaccharides (CELn), and gentiobiose (GEN2). This study reports, for the first time, four different structural states (open-unliganded, partial-open-unliganded, open-liganded and closed-liganded) of the protein βGlyBP, revealing its conformational changes upon ligand binding and suggesting a two-step induced-fit mechanism. Further, results suggest that the conformational changes of N1 and C1 subdomains drive the ligand binding, unlike that of the whole N- and C-terminal domains (NTD and CTD) as known in the "Venus Fly-trap" mechanism. Additionally, profiling of stereo-selection mechanism for α- and β-glucosides reveals that in the ligand-binding site four secondary structural elements (L1, H1, H2 and H3) drive the ligand selection. In summary, results demonstrate that the details of conformational changes and ligand selection are pre-encoded in the SBPs.

Structural analysis of β-L-arabinobiose-binding protein in the metabolic pathway of hydroxyproline-rich glycoproteins in Bifidobacterium longum

Bifidobacterium longum is a symbiotic human gut bacterium that has a degradation system for β-arabinooligosaccharides, which are present in the hydroxyproline-rich glycoproteins of edible plants. Whereas microbial degradation systems for α-linked arabinofuranosyl carbohydrates have been extensively studied, little is understood about the degradation systems targeting β-linked arabinofuranosyl carbohydrates. We functionally and structurally analyzed a substrate-binding protein (SBP) of a putative ABC transporter (BLLJ_0208) in the β-arabinooligosaccharide degradation system. Thermal shift assays and isothermal titration calorimetry revealed that the SBP specifically bound Araf-β1,2-Araf (β-Ara₂ ) with a K_d of 0.150 μm, but did not bind L-arabinose or methyl-β-Ara₂ . Therefore, the SBP was termed β-arabinobiose-binding protein (BABP). Crystal structures of BABP complexed with β-Ara₂ were determined at resolutions of up to 1.78 Å. The findings showed that β-Ara₂ was bound to BABP within a short tunnel between two lobes as an α-anomeric form at its reducing end. BABP forms extensive interactions with β-Ara₂ , and its binding mode was unique among SBPs. A molecular dynamics simulation revealed that the closed conformation of substrate-bound BABP is stable, whereas substrate-free form can adopt a fully open and two distinct semi-open states. The importer system specific for β-Ara₂ may contribute to microbial survival in biological niches with limited amounts of digestible carbohydrates. DATABASE: Atomic coordinates and structure factors (codes 6LCE and 6LCF) have been deposited in the Protein Data Bank (http://wwpdb.org/).

Structural and thermodynamic insights into β-1,2-glucooligosaccharide capture by a solute-binding protein in Listeria innocua

β-1,2-Glucans are bacterial carbohydrates that exist in cyclic or linear forms and play an important role in infections and symbioses involving Gram-negative bacteria. Although several β-1,2-glucan-associated enzymes have been characterized, little is known about how β-1,2-glucan and its shorter oligosaccharides (Sop _n s) are captured and imported into the bacterial cell. Here, we report the biochemical and structural characteristics of the Sop _n -binding protein (SO-BP, Lin1841) associated with the ATP-binding cassette (ABC) transporter from the Gram-positive bacterium Listeria innocua Calorimetric analysis revealed that SO-BP specifically binds to Sop _n s with a degree of polymerization of 3 or more, with K_d values in the micromolar range. The crystal structures of SO-BP in an unliganded open form and in closed complexes with tri-, tetra-, and pentaoligosaccharides (Sop_3-5) were determined to a maximum resolution of 1.6 Å. The binding site displayed shape complementarity to Sop _n , which adopted a zigzag conformation. We noted that water-mediated hydrogen bonds and stacking interactions play a pivotal role in the recognition of Sop_3-5 by SO-BP, consistent with its binding thermodynamics. Computational free-energy calculations and a mutational analysis confirmed that interactions with the third glucose moiety of Sop _n s are significantly responsible for ligand binding. A reduction in unfavorable changes in binding entropy that were in proportion to the lengths of the Sop _n s was explained by conformational entropy changes. Phylogenetic and sequence analyses indicated that SO-BP ABC transporter homologs, glycoside hydrolases, and other related proteins are co-localized in the genomes of several bacteria. This study may improve our understanding of bacterial β-1,2-glucan metabolism and promote the discovery of unidentified β-1,2-glucan-associated proteins.

A consensus subunit-specific model for annotation of substrate specificity for ABC transporters

A consensus classification model was built by considering three subunit proteins individually to predict the substrate specificity of ABC transporters.