Figure 6
Structural alignment of RimIMtb model (docked with peptide DP9-MARYFRR) with crystal structures of Naa50p (NatE) and TvArd1.
Cyan: RimIMtb model (developed using ITSSAR), Yellow: Substrate peptide DP9 (docked using Flexpepdock), Magenta: TvArd1 (4pV6) and Green: Naa50p (3TFY). (a) Key catalytic residues conserved between three structures and as listed in Supplementary Figure S5D, aligned at identical positions. Residues Y138 and Y139 (from Naa50p) and Y140 and Y141 (from TvArd1) (not shown in cartoon) and Y139 and Y140 of RimIMtb (shown in cartoon), aligned perfectly. E25 of RimIMtb is identified as distinctively placed in comparison with corresponding residues V29 of Naa50p and E34 of TvArd1. Hydrogen-bond between N-terminal Met of docked peptide and Y140 of RimIMtb is represented by dotted line (b) Residues involved in hydrophobic contact between RimIMtb and N-terminal Met of docked substrate peptide, defining substrate binding pocket of the enzyme (c) Surface cartoon of binding pocket of Naa50p/NatE (d) Surface cartoon of binding pocket of TvArd1 (e) Surface cartoon of binding pocket of RimIMtb.
