Kim, J., Kim, Y.J., Choi, S.Y., Lee, S.Y., Kim, K.J.
Ligand
|
Reference
Title: Structure and function of the N-terminal domain of Ralstonia eutropha polyhydroxyalkanoate synthase, and the proposed structure and mechanisms of the whole enzyme Kim YJ, Choi SY, Kim J, Jin KS, Lee SY, Kim KJ Ref: Biotechnol J, 12:, 2017 : PubMed
Polyhydroxyalkanoates (PHAs) are natural polyesters synthesized by numerous microorganisms as energy and reducing power storage materials, and have attracted much attention as substitutes for petroleum-based plastics. In an accompanying paper, the authors reported the crystal structure of the C-terminal domain of Ralstonia eutropha PHA synthase (PhaC1). Here, the authors report the 3D reconstructed model of full-length of R. eutropha PhaC1 (RePhaC1F ) by small angle X-ray scattering (SAXS) analysis. The catalytic C-terminal domain of RePhaC1 (RePhaC1CD ) dimer is located at the center of RePhaC1F , and the N-terminal domain of RePhaC1 (RePhaC1ND ) is located opposite the dimerization subdomain of RePhaC1CD , indicating that RePhaC1ND is not directly involved in the enzyme catalysis. The localization studies using RePhaC1F , RePhaC1ND and RePhaC1CD revealed that RePhaC1ND plays important roles in PHA polymerization by localizing the enzyme to the PHA granules and stabilizing the growing PHA polymer near the active site of RePhaC1CD . The serial truncation study on RePhaC1ND suggested that the predicted five alpha-helices (N-alpha3 to N-alpha7) are required for proper folding and granule binding function of RePhaC1ND . In addition, the authors also report the SAXS 3D reconstructed model of the RePhaC1F /RePhaMDeltaC complex (RePhaMDeltaC , PAKKA motif-truncated version of RePhaM). RePhaM forms a complex with RePhaC1 by interacting with RePhaC1ND and activates RePhaC1 by providing a more extensive surface area for interaction with the growing PHA polymer.
        
Title: Crystal structure of Ralstonia eutropha polyhydroxyalkanoate synthase C-terminal domain and reaction mechanisms Kim J, Kim YJ, Choi SY, Lee SY, Kim KJ Ref: Biotechnol J, 12:, 2017 : PubMed
Polyhydroxyalkanoates (PHAs) are natural polyesters synthesized by numerous microorganisms as energy and reducing power storage materials, and have attracted much attention as substitutes for petroleum-based plastics. Here, we report the first crystal structure of Ralstonia eutropha PHA synthase at 1.8 A resolution and structure-based mechanisms for PHA polymerization. RePhaC1 contains two distinct domains, the N-terminal (RePhaC1ND ) and C-terminal domains (RePhaC1CD ), and exists as a dimer. RePhaC1CD catalyzes polymerization via non-processive ping-pong mechanism using a Cys-His-Asp catalytic triad. Molecular docking simulation of 3-hydroxybutyryl-CoA to the active site of RePhaC1CD reveals residues involved in the formation of 3-hydroxybutyryl-CoA binding pocket and substrate binding tunnel. Comparative analysis with other polymerases elucidates how different classes of PHA synthases show different substrate specificities. Furthermore, we attempted structure-based protein engineering and developed a RePhaC1 mutant with enhanced PHA synthase activity.
        
Representative scheme of PHA_synth_I structure and an image from PDBsum server
no Image
Databases
PDB-Sum
5HZ2 Previously Class, Architecture, Topology and Homologous superfamily - PDB-Sum server
FSSP
5HZ2Fold classification based on Structure-Structure alignment of Proteins - FSSP server