7YX8

Crystal structure of the AM0627 (E326A) inactive mutant in complex with PSGL-1-like bis-T glycopeptide and Zn2+

Summary for 7YX8

• Entry DOI: 10.2210/pdb7yx8/pdb
• Descriptor: Peptidase M60 domain-containing protein, PSGL-1-like bis-T glycopeptide, beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose, ... (6 entities in total)
• Functional Keywords: glycoprotease, mucinase, t antigen, tn antigen, am0627, hydrolase
• Biological source: Akkermansia muciniphila; More
• Total number of polymer chains: 4
• Total formula weight: 104512.30

Authors

Taleb, V.,Liao, Q.,Narimatsu, Y.,Garcia-Garcia, A.,Companon, I.,Borges, R.J.,Gonzalez-Ramirez, A.M.,Corzana, F.,Clausen, H.,Rovira, C.,Hurtado-Guerrero, R. (deposition date: 2022-02-15, release date: 2022-07-20, Last modification date: 2024-11-13)

Primary citation

Taleb, V.,Liao, Q.,Narimatsu, Y.,Garcia-Garcia, A.,Companon, I.,Borges, R.J.,Gonzalez-Ramirez, A.M.,Corzana, F.,Clausen, H.,Rovira, C.,Hurtado-Guerrero, R.
Structural and mechanistic insights into the cleavage of clustered O-glycan patches-containing glycoproteins by mucinases of the human gut.
Nat Commun, 13:4324-4324, 2022

PubMed Abstract: Mucinases of human gut bacteria cleave peptide bonds in mucins strictly depending on the presence of neighboring O-glycans. The Akkermansia muciniphila AM0627 mucinase cleaves specifically in between contiguous (bis) O-glycans of defined truncated structures, suggesting that this enzyme may recognize clustered O-glycan patches. Here, we report the structure and molecular mechanism of AM0627 in complex with a glycopeptide containing a bis-T (Galβ1-3GalNAcα1-O-Ser/Thr) O-glycan, revealing that AM0627 recognizes both the sugar moieties and the peptide sequence. AM0627 exhibits preference for bis-T over bis-Tn (GalNAcα1-O-Ser/Thr) O-glycopeptide substrates, with the first GalNAc residue being essential for cleavage. AM0627 follows a mechanism relying on a nucleophilic water molecule and a catalytic base Glu residue. Structural comparison among mucinases identifies a conserved Tyr engaged in sugar-π interactions in both AM0627 and the Bacteroides thetaiotaomicron BT4244 mucinase as responsible for the common activity of these two mucinases with bis-T/Tn substrates. Our work illustrates how mucinases through tremendous flexibility adapt to the diversity in distribution and patterns of O-glycans on mucins.

PubMed: 35882872
DOI: 10.1038/s41467-022-32021-9

Experimental method

X-RAY DIFFRACTION (1.5 Å)