PDBsum entry 4jie

Hydrolase

PDB id: 4jie

Contents

Protein chain

484 a.a.

Ligands

GOL ×6

EPE

BMA

Waters ×231

PDB id:

4jie

Name:

Hydrolase

Title:

Structural analysis and insights into glycon specificity of the rice gh1 os7bglu26 beta-d-mannosidase

Structure:

Beta-mannosidase/beta-glucosidase. Chain: a. Engineered: yes

Source:

Oryza sativa indica group. Indian rice. Organism_taxid: 39946. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.45Å R-factor: 0.155 R-free: 0.195

Authors:

A.Tankrathok,S.Luang,R.C.Robinson,A.Kimura,M.Hrmova,J.R.Ketudat Cairns

Key ref:

A.Tankrathok et al. (2013). Structural analysis and insights into the glycon specificity of the rice GH1 Os7BGlu26 β-D-mannosidase. Acta Crystallogr D Biol Crystallogr, 69, 2124-2135. PubMed id: 24100330 DOI: 10.1107/S0907444913020568

Date:

05-Mar-13 Release date: 09-Oct-13

Protein chain

A2YPH1  (A2YPH1_ORYSI) -  Beta-glucosidase from Oryza sativa subsp. indica

Seq: 510 a.a.

Struc: 484 a.a.*

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.2.1.25 - beta-mannosidase.
• Reaction: Hydrolysis of terminal, non-reducing beta-D-mannose residues in beta-D-mannosides.

DOI no: 10.1107/S0907444913020568

Acta Crystallogr D Biol Crystallogr 69:2124-2135 (2013)

PubMed id: 24100330

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

A.Tankrathok, J.Iglesias-Fernández, S.Luang, R.C.Robinson, A.Kimura, C.Rovira, M.Hrmova, J.R.Ketudat Cairns.

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.