7BZM

Crystal structure of rice Os3BGlu7 with glucoimidazole

Summary for 7BZM

• Entry DOI: 10.2210/pdb7bzm/pdb
• Related: 2RGL
• Descriptor: Beta-glucosidase 7, GLUCOIMIDAZOLE, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ... (6 entities in total)
• Functional Keywords: gh1, rice os3bglu7, beta-glucosidase, glucoimidazole, hydrolase
• Biological source: Oryza sativa subsp. japonica (Rice)
• Total number of polymer chains: 2
• Total formula weight: 110507.34

Authors

Pengthaisong, S.,Ketudat Cairns, J.R.,Tankrathok, A. (deposition date: 2020-04-28, release date: 2020-07-08, Last modification date: 2024-10-16)

Primary citation

Nutho, B.,Pengthaisong, S.,Tankrathok, A.,Lee, V.S.,Ketudat Cairns, J.R.,Rungrotmongkol, T.,Hannongbua, S.
Structural Basis of Specific Glucoimidazole and Mannoimidazole Binding by Os3BGlu7.
Biomolecules, 10:-, 2020

PubMed Abstract: β-Glucosidases and β-mannosidases hydrolyze substrates that differ only in the epimer of the nonreducing terminal sugar moiety, but most such enzymes show a strong preference for one activity or the other. Rice Os3BGlu7 and Os7BGlu26 β-glycosidases show a less strong preference, but Os3BGlu7 and Os7BGlu26 prefer glucosides and mannosides, respectively. Previous studies of crystal structures with glucoimidazole (GIm) and mannoimidazole (MIm) complexes and metadynamic simulations suggested that Os7BGlu26 hydrolyzes mannosides via the transition state (TS) conformation preferred for mannosides and glucosides via their preferred / TS conformation. However, MIm is weakly bound by both enzymes. In the present study, we found that MIm was not bound in the active site of crystallized Os3BGlu7, but GIm was tightly bound in the -1 subsite in a / conformation via hydrogen bonds with the surrounding residues. One-microsecond molecular dynamics simulations showed that GIm was stably bound in the Os3BGlu7 active site and the glycone-binding site with little distortion. In contrast, MIm initialized in the conformation rapidly relaxed to a / conformation and moved out into a position in the entrance of the active site, where it bound more stably despite making fewer interactions. The lack of MIm binding in the glycone site in protein crystals and simulations implies that the energy required to distort MIm to the conformation for optimal active site residue interactions is sufficient to offset the energy of those interactions in Os3BGlu7. This balance between distortion and binding energy may also provide a rationale for glucosidase versus mannosidase specificity in plant β-glycosidases.

PubMed: 32549280
DOI: 10.3390/biom10060907

Experimental method

X-RAY DIFFRACTION (2.3 Å)