PDBsum entry 4zod

Hydrolase

PDB id: 4zod

Contents

Protein chains

720 a.a.

Ligands

BGC ×3

GOL ×7

PEG ×2

SO4

Metals

_MG ×2

Waters ×475

PDB id:

4zod

Name:

Hydrolase

Title:

Crystal structure of beta-glucosidase from listeria innocua in complex with glucose

Structure:

Lin1840 protein. Chain: a, b. Synonym: beta-glucosidase. Engineered: yes. Mutation: yes

Source:

Listeria innocua serovar 6a (strain clip 11262). Organism_taxid: 272626. Strain: clip 11262. Gene: lin1840. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.10Å R-factor: 0.170 R-free: 0.233

Authors:

M.Nakajima,R.Yoshida,A.Miyanaga,K.Abe,Y.Takahashi,N.Sugimoto, H.Toyoizumi,H.Nakai,M.Kitaoka,H.Taguchi

Key ref:

M.Nakajima et al. (2016). Functional and Structural Analysis of a β-Glucosidase Involved in β-1,2-Glucan Metabolism in Listeria innocua. Plos One, 11, e0148870. PubMed id: 26886583 DOI: 10.1371/journal.pone.0148870

Date:

06-May-15 Release date: 18-May-16

Protein chains

Q92AS9  (Q92AS9_LISIN) -  Lin1840 protein from Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)

Seq: 723 a.a.

Struc: 720 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1371/journal.pone.0148870

Plos One 11:e0148870 (2016)

PubMed id: 26886583

Functional and Structural Analysis of a β-Glucosidase Involved in β-1,2-Glucan Metabolism in Listeria innocua.

M.Nakajima, R.Yoshida, A.Miyanaga, K.Abe, Y.Takahashi, N.Sugimoto, H.Toyoizumi, H.Nakai, M.Kitaoka, H.Taguchi.

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.