Structural insights into the substrate binding sites of O-carbamoyltransferase VtdB from Streptomyces sp. NO1W98.

The O -carbamoyltransferase VtdB catalyzes the carbamoylation of venturicidin B, which is essential for the biosynthesis of the antibiotic venturicidin A. Here, the crystal structures of VtdB and VtdB in complex with the intermediate carbamoyladenylate (VtdBCAO) were determined at resolutions of 2.99 Å and 2.90 Å, respectively. The structures resemble the conserved YrdC-like and specific Kae1-like domains. A magnesium ion and the intermediate carbamoyladenylate were also observed in the Kae1-like domain of VtdB. The structure of VtdBCAO in complex with the substrate venturicidin B was modeled by a molecular docking method to better understand the substrate binding mode, revealing a novel venturicidin B binding pocket. • The crystal structures of VtdB and VtdB in complex with the intermediate carbamoyladenylate (VtdBCAO) are determined. • The magnesium ion binds in the Kael-like domain, which is necessary to catalyze the synthesis of venturicidin A. • The intermediate carbamoyladenylate fits tightly into a pocket of the Kae1-like domain in VtdB and VtdBCAO. • The model complex structure of the VtdBCAO−VentB predicts the binding mode of the substrate VentB. [ABSTRACT FROM AUTHOR]