5XFM

Crystal structure of beta-arabinopyranosidase

Summary for 5XFM

• Entry DOI: 10.2210/pdb5xfm/pdb
• Descriptor: Alpha-glucosidase, CALCIUM ION (3 entities in total)
• Functional Keywords: arabinopyranosidase, hydrolase
• Biological source: Bacteroides thetaiotaomicron
• Total number of polymer chains: 4
• Total formula weight: 293010.94

Authors

Kato, K.,Okuyama, M.,Yao, M. (deposition date: 2017-04-10, release date: 2018-02-28, Last modification date: 2023-11-22)

Primary citation

Kikuchi, A.,Okuyama, M.,Kato, K.,Osaki, S.,Ma, M.,Kumagai, Y.,Matsunaga, K.,Klahan, P.,Tagami, T.,Yao, M.,Kimura, A.
A novel glycoside hydrolase family 97 enzyme: Bifunctional beta-l-arabinopyranosidase/ alpha-galactosidase from Bacteroides thetaiotaomicron.
Biochimie, 142:41-50, 2017

PubMed Abstract: Glycoside hydrolase family 97 (GH97) is one of the most interesting glycosidase families, which contains inverting and retaining glycosidases. Currently, only two enzyme types, α-glucoside hydrolase and α-galactosidase, are registered in the carbohydrate active enzyme database as GH97 function-known proteins. To explore new specificities, BT3661 and BT3664, which have distinct amino acid sequences when compared with that of GH97 α-glucoside hydrolase and α-galactosidase, were characterized in this study. BT3664 was identified to be an α-galactosidase, whereas BT3661 exhibits hydrolytic activity toward both β-l-arabinopyranoside and α-d-galactopyranoside, and thus we designate BT3661 as a β-l-arabinopyranosidase/α-d-galactosidase. Since this is the first dual substrate specificity enzyme in GH97, we investigated the substrate recognition mechanism of BT3661 by determining its three-dimensional structure and based on this structural data generated a number of mutants to probe the enzymatic mechanism. Structural comparison shows that the active-site pocket of BT3661 is similar to GH97 α-galactosidase BT1871, but the environment around the hydroxymethyl group of the galactopyranoside is different. While BT1871 bears Glu361 to stabilize the hydroxy group of C6 through a hydrogen bond with its carboxy group, BT3661 has Asn338 at the equivalent position. Amino acid mutation analysis indicates that the length of the side chain at Asn338 is important for defining specificity of BT3661. The k/K value for the hydrolysis of p-nitrophenyl α-galactoside decreases when Asn338 is substituted with Glu, whereas an increase is observed when the mutation is Ala. Interestingly, mutation of Asn338 to Ala reduces the k/K value for hydrolysis of p-nitrophenyl β-l-arabinopyranoside.

PubMed: 28804002
DOI: 10.1016/j.biochi.2017.08.003

Experimental method

X-RAY DIFFRACTION (2.3 Å)