5MLX

Open loop conformation of PhaZ7 Y105E mutant

Summary for 5MLX

• Entry DOI: 10.2210/pdb5mlx/pdb
• Descriptor: PHB depolymerase PhaZ7, CHLORIDE ION, SODIUM ION, ... (4 entities in total)
• Functional Keywords: depolymerase, conformational change, biopolymer degradation, hydrolase
• Biological source: Paucimonas lemoignei
• Total number of polymer chains: 2
• Total formula weight: 74734.03

Authors

Kellici, T.,Mavromoustakos, T.,Jendrossek, D.,Papageorgiou, A.C. (deposition date: 2016-12-08, release date: 2017-05-10, Last modification date: 2024-11-20)

Primary citation

Kellici, T.F.,Mavromoustakos, T.,Jendrossek, D.,Papageorgiou, A.C.
Crystal structure analysis, covalent docking, and molecular dynamics calculations reveal a conformational switch in PhaZ7 PHB depolymerase.
Proteins, 85:1351-1361, 2017

PubMed Abstract: An open and a closed conformation of a surface loop in PhaZ7 extracellular poly(3-hydroxybutyrate) depolymerase were identified in two high-resolution crystal structures of a PhaZ7 Y105E mutant. Molecular dynamics (MD) simulations revealed high root mean square fluctuations (RMSF) of the 281-295 loop, in particular at residue Asp289 (RMSF 7.62 Å). Covalent docking between a 3-hydroxybutyric acid trimer and the catalytic residue Ser136 showed that the binding energy of the substrate is significantly more favorable in the open loop conformation compared to that in the closed loop conformation. MD simulations with the substrate covalently bound depicted 1 Å RMSF higher values for the residues 281-295 in comparison to the apo (substrate-free) form. In addition, the presence of the substrate in the active site enhanced the ability of the loop to adopt a closed form. Taken together, the analysis suggests that the flexible loop 281-295 of PhaZ7 depolymerase can act as a lid domain to control substrate access to the active site of the enzyme. Proteins 2017; 85:1351-1361. © 2017 Wiley Periodicals, Inc.

PubMed: 28370478
DOI: 10.1002/prot.25296

Experimental method

X-RAY DIFFRACTION (1.6 Å)