9J1U

Structural basis of the bifunctionality of M. salinexigens ZYF650T glucosylglycerol phosphorylase in glucosylglycerol catabolism

Summary for 9J1U

• Entry DOI: 10.2210/pdb9j1u/pdb
• Descriptor: Sucrose phosphorylase, alpha-D-glucopyranose, GLYCEROL, ... (6 entities in total)
• Functional Keywords: glucosylglycerol;phosphorylase-gh13_18;structure-double displacement mechanism, structural protein
• Biological source: Marinobacter salinexigens
• Total number of polymer chains: 6
• Total formula weight: 331109.42

Authors

Lu, D.,Ma, H.L. (deposition date: 2024-08-05, release date: 2025-09-10)

Primary citation

Lu, D.,Zhang, K.,Cheng, C.,Wu, D.,Yin, L.,Luo, Q.,Shi, M.,Ma, H.,Lu, X.
Structural basis of the bifunctionality of Marinobacter salinexigens ZYF650 T glucosylglycerol phosphorylase in glucosylglycerol catabolism.
J.Biol.Chem., 301:108127-108127, 2025

PubMed Abstract: 2-O-α-Glucosylglycerol (GG) is a natural heteroside synthesized by many cyanobacteria and a few heterotrophic bacteria under salt stress conditions. Bacteria produce GG in response to stimuli and degrade it once the stimulus diminishes. Heterotrophic bacteria utilize GG phosphorylase (GGP), a member of the GH13_18 family, via a two-step process consisting of phosphorolysis and hydrolysis for GG catabolism. However, the precise mechanism by which GGP degrades GG remains elusive. We determined the 3D structure of a recently identified GGP (MsGGP) of the deep-sea bacterium Marinobacter salinexigens ZYF650, in complex with glucose and glycerol, α-d-glucose-1-phosphate (αGlc1-P), and orthophosphate (inorganic phosphate) at resolutions of 2.5, 2.7, and 2.7 Å, respectively. Notably, the first αGlc1-P complex structure in the GH13_18 family, the complex of MsGGP and αGlc1-P, validates that GGP catalyzes GG decomposition through consecutive phosphorolysis and hydrolysis. In addition, the structure reveals the mechanism of high stereoselectivity on αGlc1-P. Glu231 and Asp190 were identified as the catalytic residues. Interestingly, these structures closely resemble each other, indicating minimal conformational changes upon binding end-product glucose and glycerol, or the intermediate αGlc1-P. The structures also indicate that the substrates may follow a specific trajectory and a precise order toward the active center in close proximity and in a geometrically favorable orientation for catalysis in a double displacement mechanism.

PubMed: 39725037
DOI: 10.1016/j.jbc.2024.108127

Experimental method

X-RAY DIFFRACTION (2.72 Å)