4JIE

Structural analysis and insights into glycon specificity of the rice GH1 Os7BGlu26 beta-D-mannosidase

Summary for 4JIE

• Entry DOI: 10.2210/pdb4jie/pdb
• Related: 4JHO
• Descriptor: Beta-mannosidase/beta-glucosidase, GLYCEROL, 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID, ... (5 entities in total)
• Functional Keywords: glycoside hydrolase family 1, beta-d-mannosidase, oryza sativa, tim barrel, glycoside hydrolase, hydrolase
• Biological source: Oryza sativa Indica Group (Indian rice)
• Total number of polymer chains: 1
• Total formula weight: 58746.83

Authors

Tankrathok, A.,Luang, S.,Robinson, R.C.,Kimura, A.,Hrmova, M.,Ketudat Cairns, J.R. (deposition date: 2013-03-05, release date: 2013-10-09, Last modification date: 2023-11-08)

Primary citation

Tankrathok, A.,Iglesias-Fernandez, J.,Luang, S.,Robinson, R.C.,Kimura, A.,Rovira, C.,Hrmova, M.,Ketudat Cairns, J.R.
Structural analysis and insights into the glycon specificity of the rice GH1 Os7BGlu26 beta-D-mannosidase
Acta Crystallogr.,Sect.D, 69:2124-2135, 2013

PubMed Abstract: Rice Os7BGlu26 is a GH1 family glycoside hydrolase with a threefold higher kcat/Km value for 4-nitrophenyl β-D-mannoside (4NPMan) compared with 4-nitrophenyl β-D-glucoside (4NPGlc). To investigate its selectivity for β-D-mannoside and β-D-glucoside substrates, the structures of apo Os7BGlu26 at a resolution of 2.20 Å and of Os7BGlu26 with mannose at a resolution of 2.45 Å were elucidated from isomorphous crystals in space group P212121. The (β/α)8-barrel structure is similar to other GH1 family structures, but with a narrower active-site cleft. The Os7BGlu26 structure with D-mannose corresponds to a product complex, with β-D-mannose in the (1)S5 skew-boat conformation. Docking of the (1)S3, (1)S5, (2)SO and (3)S1 pyranose-ring conformations of 4NPMan and 4NPGlc substrates into the active site of Os7BGlu26 indicated that the lowest energies were in the (1)S5 and (1)S3 skew-boat conformations. Comparison of these docked conformers with other rice GH1 structures revealed differences in the residues interacting with the catalytic acid/base between enzymes with and without β-D-mannosidase activity. The mutation of Tyr134 to Trp in Os7BGlu26 resulted in similar kcat/Km values for 4NPMan and 4NPGlc, while mutation of Tyr134 to Phe resulted in a 37-fold higher kcat/Km for 4NPMan than 4NPGlc. Mutation of Cys182 to Thr decreased both the activity and the selectivity for β-D-mannoside. It was concluded that interactions with the catalytic acid/base play a significant role in glycon selection.

PubMed: 24100330
DOI: 10.1107/S0907444913020568

Experimental method

X-RAY DIFFRACTION (2.45 Å)