   3.1.1.53 | apo-enzyme (PDB: 3CL4) or mutant S40A in complex with 5-N-acetyl-4,9-di-O-acetylneuraminic acid alpha-methylglycoside (PDB: 3CL5), hanging drop vapour diffusion, 18°C, 2 weeks, precipitant: 16% polyethylene glycol 8000 and 20% glycerol or 10% polyethylene glycol 3350, hexagonal bipyramide crystals: space groups: P6(5)22, unit cell parameter: a, b: 88.8-89.3, c: 280.4-282.4, soaking with 7 mM 5-N-acetyl-4,9-di-O-acetylneuraminic acid alpha-methylglycoside, molecular replacement using PDB: 1FLC (for apo-enzyme) or wild-type structure (for S40A mutant) as template, three domains: receptor-binding domain (R), acetylase domain (E, strictly conserved), and membrane-proximal domain (MP), homodimer of 2fold crystallographic symmetry with 2 major contact regions (CR1: bridges R domains, CR2: involves MP), disorder of residues 377-388, E-domain: SGNH-hydrolase fold, active site with catalytic triad (Ser40, His329, Asp326) and oxyanion hole (Asn104, Ser40, Gly75), highly variable surface loop (residues 47-54) is site of antigenic variation, R-domain: different from those of hemagglutinin-esterase fusion (HEF) and agglutinin (HA) (plasticity), binding of ligand in opposite orientation involving residues Leu212, Asn214, Ser213, Tyr184, Phe211, Leu266, Leu267 (hydrophobic pocket), coordination of potassium and water by Asp220, Ser221, Gln222, Ser263, Glu265, Leu267 |
| 3.1.1.53 | molecular modelling using PDB: 1FLC, and alpha-methyl or beta-methyl glycosides of 9-acetamido-9-deoxy-N-acetylneuraminic acid or N-acetyl-9-O-acetyl-2,6-alpha-S-glucosyl-neuraminic acid alpha-methylglycoside as substrates, no interaction between aglycon moiety and the enzyme or its active site, catalytic triad: Ser57, His355, Asp352, catalysis involves conformational change of Ser57 side chain in order to enable 9-O-acetyl-binding and position for nucleophilic attack on 9-O-acetate carbonyl carbon, beta-anomer substrate lacks bi-dendate interaction between C-1 carboxylate group and Asp352 and is no suitable substrate |
