Structure determination of a sugar-binding protein from the phytopathogenic bacterium<i>Xanthomonas citri</i>

Medrano, F.J.; Souza, Cacilda da Silva; Romero, Antonio; Balan, Andrea

doi:10.1107/s2053230x14006578

Cited by 9 publications

(4 citation statements)

References 37 publications

(55 reference statements)

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“…7B). To date, Xac-MalE has been classified as a putative maltose/trehalose-binding protein (37). However, the Xac-MalE gene (XAC2310) is located adjacent to a GH144 endo-␤-1,2-glucanase homolog (XAC2311) (SBP and GH144 in Fig.…”

Section: Comparison With Other Sbpsmentioning

confidence: 99%

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

Abe

Sunagawa

Terada

et al. 2018

Journal of Biological Chemistry

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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 s) are captured and imported into the bacterial cell. Here, we report the biochemical and structural characteristics of the Sop -binding protein (SO-BP, Lin1841) associated with the ATP-binding cassette (ABC) transporter from the Gram-positive bacterium Calorimetric analysis revealed that SO-BP specifically binds to Sop s with a degree of polymerization of 3 or more, with 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) were determined to a maximum resolution of 1.6 Å. The binding site displayed shape complementarity to Sop , which adopted a zigzag conformation. We noted that water-mediated hydrogen bonds and stacking interactions play a pivotal role in the recognition of Sop 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 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 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.

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Section: Comparison With Other Sbpsmentioning

confidence: 99%

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

Abe

Sunagawa

Terada

et al. 2018

Journal of Biological Chemistry

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“…A database search using the DALI server [ 22 ] revealed that CMMBP shows high structural similarity to SBPs that bind maltooligosaccharides (or other α-glucosides) and other sugar compounds ( Table 3 ). The best match was a maltose binding protein 3 from Thermotoga maritima (tmMBP3) [ 23 ] and a putative maltose/trehalose-binding protein from Xanthomonas citri (Xac-MalE) [ 24 ]. We noticed that the binding protein for CNN from Listeria monocytogenes (Lmo0181) also exhibited structural similarity to CMMBP [ 25 ].…”

Section: Resultsmentioning

confidence: 99%

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

et al. 2020

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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 Kd 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.

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“…In Escherichia coli, the genes encoding ABC transporters occupy almost 5% of the genome with about 80 distinct transporters 3 and 4% of the genome are encoded as ABC transporters in the Xanthomonas citri. 4 And in human about 50 ABC transporters are present. 5 ABC transporter proteins carry various substrates in and out of membrane to provide nutrients and efflux toxics for organism.…”

Section: Introductionmentioning

confidence: 99%

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

Guo

Shi

et al. 2015

RSC Adv.

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Members of the ATP-binding cassette (ABC) transporter family are present in three kingdoms of life and play a vital role in most cellular functions. ABC transporters function as either importers that bring nutrients and other molecules into cells, or as exporters that pump toxins, drugs and lipids across membranes. Currently, the limitation of 3D structures highlights the importance of the functional annotation for transporters using bioinformatics-based methods. In this work, we focused on annotation of substrate specificity for ABC transporters. Three types of the subunit proteins of ABC transporters, namely permease protein, ATPbinding protein and substrate binding protein all contribute much to the transport process, but have unique structures and properties. However previous computational methods have only considered the three subunit proteins in the same way and cannot individually characterize each type of subunit protein.Here, through individual feature evaluation and selection, specific representation for each type of subunit protein was implemented. Then three subunit-specific models were built to consistently analyse four major classes of ABC transporters with different transport targets. Our method achieved a 5-fold cross validation accuracy of 93.35%, 84.34%, 87.24% and 81.96% for sugar transporter, ion transporter, amino acid/protein transporter and others, respectively. Our method also showed an overall prediction accuracy of 88.02% with a Mathew's correlation coefficient of 0.6736 on an independent dataset. The results suggest that considering three subunit proteins separately and developing individual models for three substrate protein groups are recommendable. This method would be an effective tool for computational annotation of substrate specificity for ABC transporters.

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

Cited by 9 publications

References 37 publications

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

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

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

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

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