Additional file 2 of Determinants of substrate specificity in a catalytically diverse family of acyl-ACP thioesterases from plants

Additional file 2: Fig. S1. Predicted catalytic and acyl-binding cavity residues in modelled ALTs align with those of E. coli YbgC and Umbellularia californica FatB [45, 46, 48]. A. Monomer models of the hot-dog fold domains of MtALT1 and the E. coli acyl-CoA thioesterase YbgC, with numbered α-helices and β-strands. ALT monomers were modelled by AlphaFold 2.0, and the crystal structure of E. coli YbgC was retrieved from the RCSB PDB (PDB ID: 5 T06) [39, 40, 45]. B. Superimposition of Arabidopsis thaliana ALT3/4, Medicago truncatula ALT1/2, and Zea mays ALT1/3 homotetramer models assembled with HSYMDOCK (grey) with the crystal structure of the E. coli acyl-CoA thioesterase YbgC (yellow) [39–41, 45]. C. Comparison of predicted catalytic residues in modelled ALTs and the crystal structure of EcYbgC. AtALT4 is used as a representative example. Catalytic triad residues belong to two neighbouring subunits. D. Comparison of predicted acyl-binding cavity structure in modelled ALTs, and the crystal structures of EcYbgC and UcFatB. MtALT1 is used as a representative example. Ribbon structure of α1-α2 of the hot-dog fold domain is hidden from models to increase visibility of key residues. The crystal structure of UcFatB was retrieved from the RCSB PDB (PDB ID: 5X04), and the N-terminal hot-dog fold domain (residues 100–247) were isolated in ChimeraX 1.2.5 software. Top: Predicted substrate-binding cavity residues of MtALT1 and EcYbgC are shown as stick models. Middle: Molecular surfaces formed by predicted acyl binding cavity residues are coloured according to hydrophobicity (yellow = hydrophobic, white = amphipathic, blue = hydrophilic). Bottom: Predicted substrate-binding cavity residues of MtALT1, and experimentally determined substrate-binding cavity residues of UcFatB are shown as stick models [48]. E. Alignment of the MtALT1, EcYbgC, and N-terminal UcFatB hot-dog fold domain sequences [55]. Acyl-binding cavity residues belonging to each protein are highlighted in red [46]. Asterisks (*) indicate predicted acyl-binding cavity-forming residues of MtALT1 that align with those of both EcYbgC and UcFatB. Dots (●) indicate cavity-forming residues of MtALT1 that align with those of EcYbgC, but not UcFatB. Diamonds (◊) indicate cavity-forming residues of UcFatB that align structurally, but not on the sequence alignment, with those of MtALT1.

Récupéré en direct depuis OpenAlex et désinversé. Les résumés ne sont pas conservés dans cette base de données : les index inversés représentent 8,6 Go des 9,3 Go de texte de la base, et le serveur dispose de 13 Go libres.