8DF2

The structure of the 'ALT' construct of the Amuc_1438 glycopeptidase

Summary for 8DF2

• Entry DOI: 10.2210/pdb8df2/pdb
• Descriptor: NPCBM/NEW2 domain-containing protein, ZINC ION, CALCIUM ION, ... (5 entities in total)
• Functional Keywords: glycopeptidase, hydrolase
• Biological source: Akkermansia muciniphila
• Total number of polymer chains: 4
• Total formula weight: 213685.55

Authors

Medley, B.J.,Boraston, A.B. (deposition date: 2022-06-21, release date: 2022-08-31, Last modification date: 2024-05-22)

Primary citation

Medley, B.J.,Leclaire, L.,Thompson, N.,Mahoney, K.E.,Pluvinage, B.,Parson, M.A.H.,Burke, J.E.,Malaker, S.,Wakarchuk, W.,Boraston, A.B.
A previously uncharacterized O-glycopeptidase from Akkermansia muciniphila requires the Tn-antigen for cleavage of the peptide bond.
J.Biol.Chem., 298:102439-102439, 2022

PubMed Abstract: Akkermansia muciniphila is key member of the human gut microbiota that impacts many features of host health. A major characteristic of this bacterium is its interaction with host mucin, which is abundant in the gut environment, and its ability to metabolize mucin as a nutrient source. The machinery deployed by A. muciniphila to enable this interaction appears to be extensive and sophisticated, yet it is incompletely defined. The uncharacterized protein AMUC_1438 is encoded by a gene that was previously shown to be upregulated when the bacterium is grown on mucin. This uncharacterized protein has features suggestive of carbohydrate-recognition and peptidase activity, which led us to hypothesize that it has a role in mucin depolymerization. Here, we provide structural and functional support for the assignment of AMUC_1438 as a unique O-glycopeptidase with mucin-degrading capacity. O-glycopeptidase enzymes recognize glycans but hydrolyze the peptide backbone and are common in host-adapted microbes that colonize or invade mucus layers. Structural, kinetic, and mutagenic analyses point to a metzincin metalloprotease catalytic motif but with an active site that specifically recognizes a GalNAc residue α-linked to serine or threonine (i.e., the Tn-antigen). The enzyme catalyzes hydrolysis of the bond immediately N-terminal to the glycosylated residue. Additional modeling analyses suggest the presence of a carbohydrate-binding module that may assist in substrate recognition. We anticipate that these results will be fundamental to a wider understanding of the O-glycopeptidase class of enzymes and how they may contribute to host adaptation.

PubMed: 36049519
DOI: 10.1016/j.jbc.2022.102439

Experimental method

X-RAY DIFFRACTION (2.35 Å)