The structure of DesR from Streptomyces venezuelae, a β‐glucosidase involved in macrolide activation

Abstract

Antibiotics have, indeed, altered the course of human history as is evidenced by the increase in human life expectancy since the 1940s. Many of these natural compounds are produced by bacteria that, by necessity, must have efficient self-resistance mechanisms. The methymycin/pikromycin producing species Streptomyces venezuelae, for example, utilizes b-glucosylation of its macrolide products to neutralize their effects within the confines of the cell. Once released into the environment, these compounds are activated by the removal of the glucose moiety. In S. venezuelae, the enzyme responsible for removal of the sugar from the parent compound is encoded by the desR gene and referred to as DesR. It is a secreted enzyme containing 828 amino acid residues, and it is known to be a retaining glycosidase. Here, we describe the structure of the DesR/D-glucose complex determined to 1.4-Å resolution. The overall architecture of the enzyme can be envisioned in terms of three regions: a catalytic core and two auxiliary domains. The catalytic core harbors the binding platform for the glucose ligand. The first auxiliary domain adopts a ''PA14 fold,'' whereas the second auxiliary domain contains an immunoglobulin-like fold. Asp 273 and Glu 578 are in the proper orientation to function as the catalytic base and proton donor, respectively, required for catalysis. The overall fold of the core region places DesR into the GH3 glycoside hydrolase family of enzymes. Comparison of the DesR structure with the b-glucosidase from Kluyveromyces marxianus shows that their PA14 domains assume remarkably different orientations.

Molecular cloning and expression of thermostable glucose-tolerant β-glucosidase of Penicillium funiculosum NCL1 in Pichia pastoris and its characterization

“…The fibronectin domain found at the C-terminal end is believed to provide thermostability to the protein by managing the relative movements of C and N-terminal domains [11]. The GH3-specific catalytic residues Asp 273 and Glu 502 most likely form the substrate-binding pocket [34]. The characteristic hydrophobic cluster of GH3 β-glucosidase, 221-LYL-WPF-228 reinforced the predictions.…”

Aspergillus niger β-Glucosidase Has a Cellulase-like Tadpole Molecular Shape

“…The multiple sequence analysis was performed based on the amino acid sequences of ␤-glucosidase 1 from the following: A. niger (AnBgl1); ␤-glucosidase 1 from A. aculeatus (AaBgl1) (14); thermostable ␤-glucosidase 1 from T. aurantiacus (TaBgl1) (21); ␤-glucosidase from H. jecorina (HjBgl) (22); ␤-glucosidase from T. neapolitana (TnBgl3B) (8); ␤-glucosidase 1 from K. marxianus (KmBgl1) (10); and exo-␤-1,3-1,4-glucanase from H. vulgare subsp. vulgare (ExoI) (9). According to Varghese et al (12), the N-terminal domain of ExoI adopts a canonical (␤/␣) 8 -barrel fold.…”

“…The enzyme C-terminal part (amino acid residues Asn-755-His-860) of the homology model has an FnIII-like fold. Except for the insertion of the PA14 domain in KmBgl1 and the absence of an FnIII-like fold domain in ExoI, the tertiary structural arrangement and the patterns of the secondary structure of the AnBgl1 homology domains are similar to those of KmBgl1 (10), TnBgl3B (8), and ExoI (9). SAXS data analysis was performed using the merged SAXS curve (Fig.…”

“…vulgare (ExoI) (9). Clustal X was used for alignment (23), and refinement was carried out with Bioedit sequence tool.…”

Structural and Functional Characterization of a Ruminal β-Glycosidase Defines a Novel Subfamily of Glycoside Hydrolase Family 3 with Permuted Domain Topology

“…The later reported structures from T. neapolitana (8), Trichoderma reesei (12), Aspergillus (13, 14), and L. innocua (18) β-glucosidases, and a β-glucosidase isolated from soil compost (32), showed the presence of an additional fibronectin type III (FnIII) domain (also designated fibronectin-like domain or FLD) located at the C terminus. This three-domain arrangement is shared by other reported β-glucosidases from K. marxianus (9) and Streptomyces venezuelae (11) that also contain an additional PA14 domain inserted within the same loop of their (α/β) 6 -sandwich, although both are arranged in a different orientation. Moreover, the structure of the Pseudoalteromonas sp.…”