Loop 422–437 in NanA from Streptococcus pneumoniae plays the role of an active site lid and is associated with allosteric regulation

Abstract

Neuraminidase A from Streptococcus pneumoniae (NanA) is considered a potentially key pathogenicity factor and a promising drug target to treat human infectious diseases. Computational and experimental efforts are increasingly being used to study its structure and function which yet remain poorly understood. In this work, we characterized structural dynamics of NanA's active site and gained novel mechanistic insights into its implications for a ligand binding. We based our study on supercomputer modeling and bioinformatic analysis with a help of crystallographic data and by bringing together previously published experimental data. The most prominent conformational plasticity was observed in the loop 422–437, accompanied by the mobility of adjacent loops 352–360 and 579–587. These structural elements had been undergoing spontaneous fluctuations apparently playing the role of an active site lid: an “open” state allowed substrate access to the active site, while a “closed” state accommodated the substrate in a catalytically favorable orientation. We observed that conformational plasticity of the loop 422–437 promoted the formation of an additional pocket located between catalytic and insertion domains of the enzyme. We recently argued this site was able to bind isoprenylated flavone artocarpin as an inhibitor of pneumococcal biofilm formation. Here we showed that accommodation of the mixed-type inhibitor artocarpin in this pocket limited mobility of the loop 422–437. This represents a plausible explanation of artocarpin's regulatory effect on the enzyme's catalytic function which seems to be independent of its role in preventing biofilm formation.