6RKJ

The crystal structure of AbnE, an arabino-oligosaccharide binding protein, in complex with arabinooctaose

Summary for 6RKJ

• Entry DOI: 10.2210/pdb6rkj/pdb
• Related: 6RJY 6RKH
• Descriptor: Arabino-oligosaccharids-binding protein, alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose-(1-5)-alpha-L-arabinofuranose, GLYCEROL, ... (5 entities in total)
• Functional Keywords: geobacillus stearothermophilus, arabino-oligosaccharide, arabinohexaose, abc transporter, sugar binding protein
• Biological source: Geobacillus stearothermophilus
• Total number of polymer chains: 1
• Total formula weight: 49724.81

Authors

Lansky, S.,Salama, R.,Shoham, Y.,Shoham, G. (deposition date: 2019-04-30, release date: 2020-04-15, Last modification date: 2024-01-24)

Primary citation

Lansky, S.,Salama, R.,Shulami, S.,Lavid, N.,Sen, S.,Schapiro, I.,Shoham, Y.,Shoham, G.
Carbohydrate-Binding Capability and Functional Conformational Changes of AbnE, an Arabino-oligosaccharide Binding Protein.
J.Mol.Biol., 432:2099-2120, 2020

PubMed Abstract: ABC importers are membrane proteins responsible for the transport of nutrients into the cells of prokaryotes. Although the structures of ABC importers vary, all contain four conserved domains: two nucleotide-binding domains (NBDs), which bind and hydrolyze ATP, and two transmembrane domains (TMDs), which help translocate the substrate. ABC importers are also dependent on an additional protein component, a high-affinity substrate-binding protein (SBP) that specifically binds the target ligand for delivery to the appropriate ABC transporter. AbnE is a SBP belonging to the ABC importer for arabino-oligosaccharides in the Gram-positive thermophilic bacterium Geobacillus stearothermophilus. Using isothermal titration calorimetry (ITC), purified AbnE was shown to bind medium-sized arabino-oligosaccharides, in the range of arabino-triose (A3) to arabino-octaose (A8), all with K values in the nanomolar range. We describe herein the 3D structure of AbnE in its closed conformation in complex with a wide range of arabino-oligosaccharide substrates (A2-A8). These structures provide the basis for the detailed structural analysis of the AbnE-sugar complexes, and together with complementary quantum chemical calculations, site-specific mutagenesis, and isothermal titration calorimetry (ITC) experiments, provide detailed insights into the AbnE-substrate interactions involved. Small-angle X-ray scattering (SAXS) experiments and normal mode analysis (NMA) are used to study the conformational changes of AbnE, and these data, taken together, suggest clues regarding its binding mode to the full ABC importer.

PubMed: 32067952
DOI: 10.1016/j.jmb.2020.01.041

Experimental method

X-RAY DIFFRACTION (1.601 Å)