9FZ0

Crystal structure of SusG from Bacteroides thetaiotaomicron covalently bound to alpha-1,6 branched pseudo-trisaccharide activity-based probe

This is a non-PDB format compatible entry.

Summary for 9FZ0

• Entry DOI: 10.2210/pdb9fz0/pdb
• Related: 9FYZ
• Descriptor: Alpha-amylase SusG, alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose, (1~{S},4~{S},5~{R})-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol, ... (9 entities in total)
• Functional Keywords: glycoside hydrolase, amylase, hydrolase
• Biological source: Bacteroides thetaiotaomicron
• Total number of polymer chains: 2
• Total formula weight: 158042.69

Authors

Pickles, I.B.,Moroz, O.,Davies, G. (deposition date: 2024-07-04, release date: 2024-12-11, Last modification date: 2025-02-05)

Primary citation

Pickles, I.B.,Chen, Y.,Moroz, O.,Brown, H.A.,de Boer, C.,Armstrong, Z.,McGregor, N.G.S.,Artola, M.,Codee, J.D.C.,Koropatkin, N.M.,Overkleeft, H.S.,Davies, G.J.
Precision Activity-Based alpha-Amylase Probes for Dissection and Annotation of Linear and Branched-Chain Starch-Degrading Enzymes.
Angew.Chem.Int.Ed.Engl., 64:e202415219-e202415219, 2025

PubMed Abstract: α-Amylases are the workhorse enzymes of starch degradation. They are central to human health, including as targets for anti-diabetic compounds, but are also the key enzymes in the industrial processing of starch for biofuels, corn syrups, brewing and detergents. Dissection of the activity, specificity and stability of α-amylases is crucial to understanding their biology and allowing their exploitation. Yet, functional characterization lags behind DNA sequencing and genomics; and new tools are required for rapid analysis of α-amylase function. Here, we design, synthesize and apply new branched α-amylase activity-based probes. Using both α-1,6 branched and unbranched α-1,4 maltobiose activity-based probes we were able to explore the stability and substrate specificity of both a panel of human gut microbial α-amylases and a panel of industrially relevant α-amylases. We also demonstrate how we can detect and annotate the substrate specificity of α-amylases in the complex cell lysate of both a prominent gut microbe and a diverse compost sample by in-gel fluorescence and mass spectrometry. A toolbox of starch-active activity-based probes will enable rapid functional dissection of α-amylases. We envisage activity-based probes contributing to better selection and engineering of enzymes for industrial application as well as fundamental analysis of enzymes in human health.

PubMed: 39601378
DOI: 10.1002/anie.202415219

Experimental method

X-RAY DIFFRACTION (2.65 Å)