| Summary: | Structure analysis and ensemble refinement of the apo-structure of thymidine
diphosphate (TDP)-rhamnose 3′-O-methyltransferase reveal
a gate for substrate entry and product release. TDP-rhamnose
3′-O-methyltransferase (CalS11) catalyses a
3′-O-methylation of TDP-rhamnose, an intermediate in
the biosynthesis of enediyne antitumor antibiotic calicheamicin. CalS11 operates
at the sugar nucleotide stage prior to glycosylation step. Here, we present the
crystal structure of the apo form of CalS11 at 1.89 Å resolution.
We propose that the L2 loop functions as a gate facilitating and/or providing
specificity for substrate entry or promoting product release. Ensemble
refinement analysis slightly improves the crystallographic refinement statistics
and furthermore provides a compelling way to visualize the dynamic model of loop
L2, supporting the understanding of its proposed role in catalysis.
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