The crystal structure of the outer membrane lipoprotein YbhC from Escherichia coli sheds new light on the phylogeny of carbohydrate esterase family 8.

摘要

INTRODUCTION The functional characterization of the totality of Esche-richia coli gene products by transcriptomic, proteomic, biochemical, and structural techniques remains a noble goal in the "postgenomic" era. As a model organism, E. coli is the best characterized species from a molecular perspective: Of 4460 genes, 66% have been functionally annotated based on experimental observations, as of 2007.1 Even so, over 1000 genes are still of unknown function, including the outer membrane (OM) lipopro-tein YbhC,2'3 which has been classified as a member of carbohydrate esterase family 8 (CE8) in the renown carbohydrate active enzymes (CAZy) database. All CE8 proteins that have been biochemically characterized thus far, including bacterial, plant, and fungal representatives, have been shown to be pectin methyles-terases (PMEs, EC 3.1.1.11). On the basis of the sequence similarity reflected in its CE8 grouping, YbhC has previously been annotated as a PME or, alternately, as a pal-mitoyl-CoA thioesterase, the latter based on results from a high-throughput enzyme activity screen. Interestingly, phylogenetic analysis indicates that E. coli YbhC and homologs from other gram-negative Enterobacteriaceae form a distinct clade in CE8, which is well-separated from those containing demonstrated bacterial PMEs. This observation, coupled with the ambiguous functional assignment of YbhC, motivated the solution of the tertiary structure of YbhC and a re-examination of its enzyme activity in this context.