4ZOA

Crystal Structure of beta-glucosidase from Listeria innocua in complex with isofagomine

Summary for 4ZOA

• Entry DOI: 10.2210/pdb4zoa/pdb
• Related: 4ZO6 4ZO7 4ZO8 4ZO9 4ZOB 4ZOC 4ZOD 4ZOE
• Descriptor: Lin1840 protein, 5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: tim barrel, hydrolase, beta-1, 2-glucan degradation, cytosol
• Biological source: Listeria innocua serovar 6a (strain CLIP 11262)
• Total number of polymer chains: 2
• Total formula weight: 161681.15

Authors

Nakajima, M.,Yoshida, R.,Miyanaga, A.,Abe, K.,Takahashi, Y.,Sugimoto, N.,Toyoizumi, H.,Nakai, H.,Kitaoka, M.,Taguchi, H. (deposition date: 2015-05-06, release date: 2016-05-18, Last modification date: 2023-11-08)

Primary citation

Nakajima, M.,Yoshida, R.,Miyanaga, A.,Abe, K.,Takahashi, Y.,Sugimoto, N.,Toyoizumi, H.,Nakai, H.,Kitaoka, M.,Taguchi, H.
Functional and Structural Analysis of a beta-Glucosidase Involved in beta-1,2-Glucan Metabolism in Listeria innocua
Plos One, 11:e0148870-e0148870, 2016

PubMed Abstract: Despite the presence of β-1,2-glucan in nature, few β-1,2-glucan degrading enzymes have been reported to date. Recently, the Lin1839 protein from Listeria innocua was identified as a 1,2-β-oligoglucan phosphorylase. Since the adjacent lin1840 gene in the gene cluster encodes a putative glycoside hydrolase family 3 β-glucosidase, we hypothesized that Lin1840 is also involved in β-1,2-glucan dissimilation. Here we report the functional and structural analysis of Lin1840. A recombinant Lin1840 protein (Lin1840r) showed the highest hydrolytic activity toward sophorose (Glc-β-1,2-Glc) among β-1,2-glucooligosaccharides, suggesting that Lin1840 is a β-glucosidase involved in sophorose degradation. The enzyme also rapidly hydrolyzed laminaribiose (β-1,3), but not cellobiose (β-1,4) or gentiobiose (β-1,6) among β-linked gluco-disaccharides. We determined the crystal structures of Lin1840r in complexes with sophorose and laminaribiose as productive binding forms. In these structures, Arg572 forms many hydrogen bonds with sophorose and laminaribiose at subsite +1, which seems to be a key factor for substrate selectivity. The opposite side of subsite +1 from Arg572 is connected to a large empty space appearing to be subsite +2 for the binding of sophorotriose (Glc-β-1,2-Glc-β-1,2-Glc) in spite of the higher Km value for sophorotriose than that for sophorose. The conformations of sophorose and laminaribiose are almost the same on the Arg572 side but differ on the subsite +2 side that provides no interaction with a substrate. Therefore, Lin1840r is unable to distinguish between sophorose and laminaribiose as substrates. These results provide the first mechanistic insights into β-1,2-glucooligosaccharide recognition by β-glucosidase.

PubMed: 26886583
DOI: 10.1371/journal.pone.0148870

Experimental method

X-RAY DIFFRACTION (2.17 Å)