Structural Assignment of a Type II PHA Synthase and an Insight Into Its Catalytic Mechanism Using Human Gastric Lipase as the Modeling Template

A three dimensional (3D) model for the catalytic region of Type II Pseudomonas sp. USM 4-55 PHA synthase 1 (PhaC1$_{P.sp\;USM\;4-55}$) from residue 267 to residue 484 was developed. Sequence analysis demonstrated that PhaC1$_{P.sp\;USM\;4-55}$ lacked homology with all known structural databases. PSI-BLAST and HMM Superfamily analyses demonstrated that this enzyme belongs to the ${\alpha}/{\beta}$ hydrolase fold family. Threading approach revealed that the most suitable template to use was the Human gastric lipase (1HLG). The superimposition of the predicted PhaC1$_{P.sp\;USM\;4-55}$ model with the 1HLG template structure covering 86.2% of the backbone atoms showed an RMSD of 1.15 ${\AA}$ The catalytic residues comprising of Cys296, Asp451, His452 and His479 were found to be conserved and were located adjacent to each other. We proposed that the catalytic mechanism involved the formation of two tetrahedral intermediates.