7P1E

Structure of KDNase from Aspergillus Terrerus in complex with 2,3-difluoro-2-keto-3-deoxynononic acid

Summary for 7P1E

• Entry DOI: 10.2210/pdb7p1e/pdb
• Descriptor: Sialidase domain-containing protein, 3-deoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid, (2R,3R,4R,5R,6S)-2,3-bis(fluoranyl)-4,5-bis(oxidanyl)-6-[(1R,2R)-1,2,3-tris(oxidanyl)propyl]oxane-2-carboxylic acid, ... (7 entities in total)
• Functional Keywords: carbohydrate metabolism, enzyme structure, protein structure, kdn, kdnase, sialic acid, sialidase, carbohydrate
• Biological source: Aspergillus terreus (strain NIH 2624 / FGSC A1156)
• Total number of polymer chains: 1
• Total formula weight: 45436.16

Authors

Gloster, T.M.,McMahon, S.A. (deposition date: 2021-07-01, release date: 2021-10-20, Last modification date: 2024-10-16)

Primary citation

Nejatie, A.,Steves, E.,Gauthier, N.,Baker, J.,Nesbitt, J.,McMahon, S.A.,Oehler, V.,Thornton, N.J.,Noyovitz, B.,Khazaei, K.,Byers, B.W.,Zandberg, W.F.,Gloster, T.M.,Moore, M.M.,Bennet, A.J.
Kinetic and Structural Characterization of Sialidases (Kdnases) from Ascomycete Fungal Pathogens.
Acs Chem.Biol., 16:2632-2640, 2021

PubMed Abstract: Sialidases catalyze the release of sialic acid from the terminus of glycan chains. We previously characterized the sialidase from the opportunistic fungal pathogen, and showed that it is a Kdnase. That is, this enzyme prefers 3-deoxy-d-glycero-d-galacto-non-2-ulosonates (Kdn glycosides) as the substrate compared to -acetylneuraminides (Neu5Ac). Here, we report characterization and crystal structures of putative sialidases from two other ascomycete fungal pathogens, (S) and (S). Unlike Kdnase (S), hydrolysis with the Neu5Ac substrates was negligible for S and S; thus, S and S are selective Kdnases. The second-order rate constant for hydrolysis of aryl Kdn glycosides by S is similar to that by S but 30-fold higher by S. The structures of these glycoside hydrolase family 33 (GH33) enzymes in complex with a range of ligands for both S and S show subtle changes in ring conformation that mimic the Michaelis complex, transition state, and covalent intermediate formed during catalysis. In addition, they can aid identification of important residues for distinguishing between Kdn and Neu5Ac substrates. When , and were grown in chemically defined media, Kdn was detected in mycelial extracts, but Neu5Ac was only observed in or extracts. The C8 monosaccharide 3-deoxy-d--oct-2-ulosonic acid (Kdo) was also identified in and samples. A fluorescent Kdn probe was synthesized and revealed the localization of S in vesicles at the cell surface.

PubMed: 34724608
DOI: 10.1021/acschembio.1c00666

Experimental method

X-RAY DIFFRACTION (1.53 Å)