6lcf | pdb_00006lcf

Crystal Structure of beta-L-arabinobiose binding protein - native

spinqualitylabelsall models 6lcf, resolution 1.92Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6lcf is a 2 chain structure with sequence from As 1.2186. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: FUB Gene: APC1462_0182, APC1476_0195, APC1503_0213, APS65_00860, BBG7_0210, BL105A_0201, DPC6316_0214, DPC6317_0191, DW237_03380, DW792_04665, DWV59_05050, DWV93_04885, DWZ73_01175, EAI75_02995, HMPREF0177_01141 (AS 1.2186) Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Bifidobacterium longum is a symbiotic human gut bacterium that has a degradation system for beta-arabinooligosaccharides, which are present in the hydroxyproline-rich glycoproteins of edible plants. Whereas microbial degradation systems for alpha-linked arabinofuranosyl carbohydrates have been extensively studied, little is understood about the degradation systems targeting beta-linked arabinofuranosyl carbohydrates. We functionally and structurally analyzed a substrate-binding protein (SBP) of a putative ABC transporter (BLLJ_0208) in the beta-arabinooligosaccharide degradation system. Thermal shift assays and isothermal titration calorimetry revealed that the SBP specifically bound Araf-beta1,2-Araf (beta-Ara2 ) with a Kd of 0.150 mum, but did not bind L-arabinose or methyl-beta-Ara2 . Therefore, the SBP was termed beta-arabinobiose-binding protein (BABP). Crystal structures of BABP complexed with beta-Ara2 were determined at resolutions of up to 1.78 A. The findings showed that beta-Ara2 was bound to BABP within a short tunnel between two lobes as an alpha-anomeric form at its reducing end. BABP forms extensive interactions with beta-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 beta-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 (https://wwpdb.org/). Structural analysis of beta-L-arabinobiose-binding protein in the metabolic pathway of hydroxyproline-rich glycoproteins in Bifidobacterium longum.,Miyake M, Terada T, Shimokawa M, Sugimoto N, Arakawa T, Shimizu K, Igarashi K, Fujita K, Fushinobu S FEBS J. 2020 Apr 4. doi: 10.1111/febs.15315. PMID:32246585 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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