3PTM: The Crystal Structure Of Rice (Oryza Sativa L.) Os4bglu12 With 2- Fluoroglucopyranoside

Rice Os4BGlu12, a glycoside hydrolase family 1 (GH1) beta-glucosidase, hydrolyzes beta-(1,4)-linked oligosaccharides of 3-6 glucosyl residues and the beta-(1,3)-linked disaccharide laminaribiose, as well as certain glycosides. The crystal structures of apo Os4BGlu12, and its complexes with 2,4-dinitrophenyl-2-deoxyl-2-fluoroglucoside (DNP2FG) and 2-deoxy-2-fluoroglucose (G2F) were solved at 2.50, 2.45 and 2.40A resolution, respectively. The overall structure of rice Os4BGlu12 is typical of GH1 enzymes, but it contains an extra disulfide bridge in the loop B region. The glucose ring of the G2F in the covalent intermediate was found in a (4)C(1) chair conformation, while that of the noncovalently bound DNP2FG had a (1)S(3) skew boat, consistent with hydrolysis via a (4)H(3) half-chair transition state. The position of the catalytic nucleophile (Glu393) in the G2F structure was more similar to that of the Sinapsis alba myrosinase G2F complex than to that in covalent intermediates of other O-glucosidases, such as rice Os3BGlu6 and Os3BGlu7 beta-glucosidases. This correlated with a significant thioglucosidase activity for Os4BGlu12, although with 200- to 1200-fold lower k(cat)/K(m) values for S-glucosides than the comparable O-glucosides, while hydrolysis of S-glucosides was undetectable for Os3BGlu6 and Os3BGlu7.
PDB ID: 3PTMDownload
MMDB ID: 90630
PDB Deposition Date: 2010/12/3
Updated in MMDB: 2011/05
Experimental Method:
x-ray diffraction
Resolution: 2.4  Å
Source Organism:
Similar Structures:
Biological Unit for 3PTM: monomeric; determined by author and by software (PISA)
Molecular Components in 3PTM
Label Count Molecule
Protein (1 molecule)
Beta-glucosidase Os4bglu12
Molecule annotation
Chemicals (7 molecules)
* Click molecule labels to explore molecular sequence information.

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