5WCZ

Crystal Structure of Wild-Type MalL from Bacillus subtilis with TS analogue 1-deoxynojirimycin

Summary for 5WCZ

• Entry DOI: 10.2210/pdb5wcz/pdb
• Descriptor: Oligo-1,6-glucosidase 1, 1-DEOXYNOJIRIMYCIN, GLYCEROL, ... (4 entities in total)
• Functional Keywords: tim barrel; glucosidase; 1-deoxynojirimycin;, hydrolase
• Biological source: Bacillus subtilis
• Cellular location: Cytoplasm: O06994
• Total number of polymer chains: 2
• Total formula weight: 139073.50

Authors

Arcus, V.L.,Prentice, E.J. (deposition date: 2017-07-03, release date: 2018-03-28, Last modification date: 2023-10-04)

Primary citation

van der Kamp, M.W.,Prentice, E.J.,Kraakman, K.L.,Connolly, M.,Mulholland, A.J.,Arcus, V.L.
Dynamical origins of heat capacity changes in enzyme-catalysed reactions.
Nat Commun, 9:1177-1177, 2018

PubMed Abstract: Heat capacity changes are emerging as essential for explaining the temperature dependence of enzyme-catalysed reaction rates. This has important implications for enzyme kinetics, thermoadaptation and evolution, but the physical basis of these heat capacity changes is unknown. Here we show by a combination of experiment and simulation, for two quite distinct enzymes (dimeric ketosteroid isomerase and monomeric alpha-glucosidase), that the activation heat capacity change for the catalysed reaction can be predicted through atomistic molecular dynamics simulations. The simulations reveal subtle and surprising underlying dynamical changes: tightening of loops around the active site is observed, along with changes in energetic fluctuations across the whole enzyme including important contributions from oligomeric neighbours and domains distal to the active site. This has general implications for understanding enzyme catalysis and demonstrating a direct connection between functionally important microscopic dynamics and macroscopically measurable quantities.

PubMed: 29563521
DOI: 10.1038/s41467-018-03597-y

Experimental method

X-RAY DIFFRACTION (1.58 Å)