9SM2

Cryo-EM structure of the closed-closed dextran utilisome (BT3087-BT3090), with GHdex D297A E360A catalytic inactivation, with bound IMO4, IMO6 and IMO8

Summary for 9SM2

• Entry DOI: 10.2210/pdb9sm2/pdb
• EMDB information: 55024
• Descriptor: SusC homolog, SusD homolog, BT3088 (SGBPdex), ... (7 entities in total)
• Functional Keywords: dextran, dextranase, susd, sgbp, bacteroides, gh, glycoside hydrolase, utilisome, gh66, tbdt, membrane protein
• Biological source: Bacteroides thetaiotaomicron VPI-5482; More
• Total number of polymer chains: 8
• Total formula weight: 586078.82

Authors

Feasey, M.,Basle, A.,van den Berg, B. (deposition date: 2025-09-05, release date: 2026-07-29, Last modification date: 2026-08-19)

Primary citation

Feasey, M.,Silale, A.,Basle, A.,van den Berg, B.
Structural and functional characterisation of the dextran utilisome from Bacteroides thetaiotaomicron .
J Struct Biol X, 14:100153-100153, 2026

PubMed Abstract: () is a model Bacteroidota of the healthy human gut microbiota and a specialist in glycan utilisation. Like other , has many highly regulated polysaccharide utilisation loci (PUL) that encode outer membrane (OM) TonB-dependent transporters (SusC), closely associated "lid" lipoproteins (SusD), and additional surface-exposed lipoproteins (SLPs) that bind and partially degrade specific glycans derived from host cells, diet, or other microbiota members. The canonical starch PUL products are thought to form a dynamic complex in the presence of starch. However, other PULs form stable complexes in the absence of substrate (recently named "utilisomes"), with additional surface lipoproteins tightly associated with the core SusCD complex. In this study, we characterised the dextran utilisome, with a SusCD core and an associated glycoside hydrolase (GH) and surface glycan binding protein (SBGP). Via X-ray crystallography we solved high-resolution structures of SBGP in isolation and SusD and GH bound to dextran oligosaccharides. We used isothermal titration calorimetry (ITC) to quantify ligand binding of wild type and mutant SLPs. We further used single particle cryo-EM of the catalytically inactive dextran utilisome to visualise open and closed states of the complex. Three occupied dextran binding sites were observed across SusC, SusD and GH, with substrate observed in both open and closed states of SusD. 3D variability analysis showed a minority of particles in the process of SusD lid closure. Together our work defines commonalities and differences across utilisomes dedicated to the import of simple glycans.

PubMed: 42569704
DOI: 10.1016/j.yjsbx.2026.100153

Experimental method

ELECTRON MICROSCOPY (2.5 Å)