Fig. 4. Docking of Leu-DBE to BtCDPS. Docking experiments reveal Leu-DBE binds to BtCDPS with more favourable catalytically productive poses in the first catalytic cycle compared to the second catalytic cycle. (A) A heat map illustrating relative ΔG values (Pose 1 most favourable – pose 10 least favourable) for docking of Leu-DBE to BtCDPSApo and BtCDPSIntermediate. BtCDPSIntermediate represents an acyl-intermediate enzyme state created by superimposing PDB: 4Q24 and trimming down the ligand atoms to convert to leucine, before merging. (B) In the first catalytic cycle Leu-DBE (cyan) docks favourably to BtCDPSapo in catalytically productive poses, represented here by pose 1. The leucine moiety places into the P1 pocket (green carbon atoms), with the amide bond place between the catalytic residues, E179, S33 and Y175 (yellow carbon atoms). The nitro groups from DBE-Leu interact with S33, Y199, R153 and S152. (C) Representation of the less favourable docking pose 9. The DBE moiety occupies the P1 pocket, thus the leucine moiety is in a catalytically unproductive pose. (D) Pose 1, represents the most favourable docking pose of Leu-DBE (cyan) to BtCDPSIntermediate, which is a model of a leucyl-S33 intermediate (purple carbon atoms) occupying the P1 pocket. The Leu-DBE molecule in pose 1 binds in a catalytically unproductive manner. (E) The less favourable, pose 6, represents a catalytically productive binding pose of Leu-DBE to BtCDPSIntermediate. The leucine moiety sits in the P2 pocket (residues with orange carbon atoms) and the amide bond is within hydrogen bonding distance of the catalytic residues.
