5XXM

Crystal structure of GH3 beta-glucosidase from Bacteroides thetaiotaomicron in complex with gluconolactone

Summary for 5XXM

• Entry DOI: 10.2210/pdb5xxm/pdb
• Descriptor: Periplasmic beta-glucosidase, MAGNESIUM ION, D-glucono-1,5-lactone, ... (5 entities in total)
• Functional Keywords: glycoside hydrolase family 3, beta-glucosidase, hydrolase
• Biological source: Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482)
• Total number of polymer chains: 2
• Total formula weight: 168636.19

Authors

Nakajima, M.,Ishiguro, R.,Tanaka, N.,Abe, K.,Maeda, T.,Miyanaga, A.,Takahash, Y.,Sugimoto, N.,Nakai, H.,Taguchi, H. (deposition date: 2017-07-04, release date: 2017-12-13, Last modification date: 2024-03-27)

Primary citation

Ishiguro, R.,Tanaka, N.,Abe, K.,Nakajima, M.,Maeda, T.,Miyanaga, A.,Takahashi, Y.,Sugimoto, N.,Nakai, H.,Taguchi, H.
Function and structure relationships of a beta-1,2-glucooligosaccharide-degrading beta-glucosidase.
FEBS Lett., 591:3926-3936, 2017

PubMed Abstract: BT_3567 protein, a putative β-glucosidase from Bacteroides thetaiotaomicron, exhibits higher activity toward Sop (Sop , n: degree of polymerization of β-1,2-glucooligosaccharides) than toward Sop , unlike a known β-glucosidase from Listeria innocua which predominantly prefers Sop . In the complex structure determined by soaking of a D286N mutant crystal with Sop , a Sop moiety was observed at subsites -1 to +2. The glucose moiety at subsite +2 forms a hydrogen bond with Asn81, which is replaced with Gly in the L. innocua β-glucosidase. The K values of the N81G mutant for Sop are much higher than those of the wild-type, suggesting that Asn81 contributes to the binding to substrates longer than Sop .

PubMed: 29131329
DOI: 10.1002/1873-3468.12911

Experimental method

X-RAY DIFFRACTION (1.7 Å)