title: Crystal structure analysis, covalent docking, and molecular dynamics calculations reveal a conformational switch in PhaZ7 PHB depolymerase.
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.
authors.affiliation: Department of Chemistry, National and Kapodistrian University of Athens, Athens, 15784, Greece.|Department of Chemistry, University of Ioannina, Ioannina, 45110, Greece.
authors.forename: Tahsin F
authors.identifier: 0000-0001-6977-9946
authors.initials: TF
authors.lastname: Kellici
authors.affiliation: Department of Chemistry, National and Kapodistrian University of Athens, Athens, 15784, Greece.|Department of Chemistry, York College and the Graduate Center of the City University of New York, 94-20 Guy R. Brewer Blvd, Jamaica, New York, 11451.
authors.forename: Thomas
authors.initials: T
authors.lastname: Mavromoustakos
authors.affiliation: Institut für Mikrobiologie, Universität Stuttgart, Allmandring 31, Stuttgart, 70550, Germany.
authors.forename: Dieter
authors.initials: D
authors.lastname: Jendrossek
authors.affiliation: Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, 20521, Finland.
authors.forename: Anastassios C
authors.identifier: 0000-0002-7980-1120
authors.initials: AC
authors.lastname: Papageorgiou
mesh_terms: D020816:Amino Acid Motifs; D001412:Bacillus subtilis / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D042521:Burkholderiaceae / Q000737:chemistry* / Q000201:enzymology; D002265:Carboxylic Ester Hydrolases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D020134:Catalytic Domain; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray; D015870:Gene Expression; D006885:Hydroxybutyrates / Q000737:chemistry* / Q000378:metabolism; D007700:Kinetics; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D009154:Mutation; D011091:Polyesters / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D000072756:Protein Conformation, alpha-Helical; D000072757:Protein Conformation, beta-Strand; D054730:Protein Interaction Domains and Motifs; D017434:Protein Structure, Tertiary; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D013379:Substrate Specificity; D013816:Thermodynamics; D000094122:Polyhydroxybutyrates
chemical_list: D001426:Bacterial Proteins; D002265:Carboxylic Ester Hydrolases; D006885:Hydroxybutyrates; D011091:Polyesters; D011994:Recombinant Proteins; C003182:poly-beta-hydroxybutyrate; D000094122:Polyhydroxybutyrates; C438011:PHAZ7 protein, Paucimonas lemoignei
keywords: X-ray crystallography; biopolymer; covalent docking; depolymerase; molecular dynamics simulations