6KPM

Crystal Structure of endo-beta-N-acetylglucosaminidase from Cordyceps militaris in complex with L-fucose

Summary for 6KPM

• Entry DOI: 10.2210/pdb6kpm/pdb
• Descriptor: Chitinase, alpha-L-fucopyranose, TRIETHYLENE GLYCOL, ... (5 entities in total)
• Functional Keywords: tim barrel, hydrolase
• Biological source: Cordyceps militaris CM01 (Caterpillar fungus)
• Total number of polymer chains: 1
• Total formula weight: 33930.86

Authors

Seki, H.,Arakawa, T.,Yamada, C.,Takegawa, K.,Fushinobu, S. (deposition date: 2019-08-15, release date: 2019-10-02, Last modification date: 2024-11-13)

Primary citation

Seki, H.,Huang, Y.,Arakawa, T.,Yamada, C.,Kinoshita, T.,Iwamoto, S.,Higuchi, Y.,Takegawa, K.,Fushinobu, S.
Structural basis for the specific cleavage of core-fucosylatedN-glycans by endo-beta-N-acetylglucosaminidase from the fungusCordyceps militaris.
J.Biol.Chem., 294:17143-17154, 2019

PubMed Abstract: -Linked glycans play important roles in various cellular and immunological events. Endo-β--acetylglucosaminidase (ENGase) can release or transglycosylate -glycans and is a promising tool for the chemoenzymatic synthesis of glycoproteins with homogeneously modified glycans. The ability of ENGases to act on core-fucosylated glycans is a key factor determining their therapeutic utility because mammalian -glycans are frequently α-1,6-fucosylated. Although the biochemistries and structures of various ENGases have been studied extensively, the structural basis for the recognition of the core fucose and the asparagine-linked GlcNAc is unclear. Herein, we determined the crystal structures of a core fucose-specific ENGase from the caterpillar fungus (Endo-CoM), which belongs to glycoside hydrolase family 18. Structures complexed with fucose-containing ligands were determined at 1.75-2.35 Å resolutions. The fucose moiety linked to GlcNAc is extensively recognized by protein residues in a round-shaped pocket, whereas the asparagine moiety linked to the GlcNAc is exposed to the solvent. The -glycan-binding cleft of Endo-CoM is Y-shaped, and several lysine and arginine residues are present at its terminal regions. These structural features were consistent with the activity of Endo-CoM on fucose-containing glycans on rituximab (IgG) and its preference for a sialobiantennary substrate. Comparisons with other ENGases provided structural insights into their core fucose tolerance and specificity. In particular, Endo-F3, a known core fucose-specific ENGase, has a similar fucose-binding pocket, but the surrounding residues are not shared with Endo-CoM. Our study provides a foothold for protein engineering to develop enzymatic tools for the preparation of more effective therapeutic antibodies.

PubMed: 31548313
DOI: 10.1074/jbc.RA119.010842

Experimental method

X-RAY DIFFRACTION (1.8 Å)