8P0Q

Crystal structure of AaNGT complexed to UDP and a peptide

Summary for 8P0Q

• Entry DOI: 10.2210/pdb8p0q/pdb
• Descriptor: Adhesin, PHE-GLY-ASN-TRP-THR-THR, URIDINE-5'-DIPHOSPHATE, ... (4 entities in total)
• Functional Keywords: n-glycosylation, asn tautomeric form, aad, glycosyltransferase, gt-b, transferase
• Biological source: Aggregatibacter aphrophilus; More
• Total number of polymer chains: 4
• Total formula weight: 143877.19

Authors

Piniello, B.,Macias-Leon, J.,Rovira, C.,Hurtado-Guerrero, R. (deposition date: 2023-05-10, release date: 2023-09-06, Last modification date: 2023-09-27)

Primary citation

Piniello, B.,Macias-Leon, J.,Miyazaki, S.,Garcia-Garcia, A.,Companon, I.,Ghirardello, M.,Taleb, V.,Veloz, B.,Corzana, F.,Miyagawa, A.,Rovira, C.,Hurtado-Guerrero, R.
Molecular basis for bacterial N-glycosylation by a soluble HMW1C-like N-glycosyltransferase.
Nat Commun, 14:5785-5785, 2023

PubMed Abstract: Soluble HMW1C-like N-glycosyltransferases (NGTs) catalyze the glycosylation of Asn residues in proteins, a process fundamental for bacterial autoaggregation, adhesion and pathogenicity. However, our understanding of their molecular mechanisms is hindered by the lack of structures of enzymatic complexes. Here, we report structures of binary and ternary NGT complexes of Aggregatibacter aphrophilus NGT (AaNGT), revealing an essential dyad of basic/acidic residues located in the N-terminal all α-domain (AAD) that intimately recognizes the Thr residue within the conserved motif Asn-X-Ser/Thr. Poor substrates and inhibitors such as UDP-galactose and UDP-glucose mimetics adopt non-productive conformations, decreasing or impeding catalysis. QM/MM simulations rationalize these results, showing that AaNGT follows a S2 reaction mechanism in which the acceptor asparagine uses its imidic form for catalysis and the UDP-glucose phosphate group acts as a general base. These findings provide key insights into the mechanism of NGTs and will facilitate the design of structure-based inhibitors to treat diseases caused by non-typeable H. influenzae or other Gram-negative bacteria.

PubMed: 37723184
DOI: 10.1038/s41467-023-41238-1

Experimental method

X-RAY DIFFRACTION (2.8 Å)