4BYM

Structure of PhaZ7 PHB depolymerase Y105E mutant

Summary for 4BYM

• Entry DOI: 10.2210/pdb4bym/pdb
• Descriptor: PHB DEPOLYMERASE PHAZ7, SODIUM ION, CHLORIDE ION, ... (4 entities in total)
• Functional Keywords: hydrolase, catalytic triad, substrate-binding cavity, binding cavity, 3hb trimer binding
• Biological source: PAUCIMONAS LEMOIGNEI
• Total number of polymer chains: 2
• Total formula weight: 72487.32

Authors

Hermawan, S.,Subedi, B.,Papageorgiou, A.C.,Jendrossek, D. (deposition date: 2013-07-20, release date: 2013-09-18, Last modification date: 2024-10-23)

Primary citation

Jendrossek, D.,Hermawan, S.,Subedi, B.,Papageorgiou, A.C.
Biochemical Analysis and Structure Determination of Paucimonas Lemoignei Poly(3-Hydroxybutyrate) (Phb) Depolymerase Phaz7 Muteins Reveal the Phb Binding Site and Details of Substrate-Enzyme Interactions.
Mol.Microbiol., 90:649-, 2013

PubMed Abstract: Five amino acids (Y105, Y176, Y189, Y189, W207) that constitute the substrate binding site of PHB depolymerase PhaZ7 were identified. All residues are located at a single surface-exposed location of PhaZ7. Exchange of these amino acids by less hydrophobic, hydrophilic or negatively charged residues reduced binding of PhaZ7 to PHB. Modifications of other residues at the PhaZ7 surface (F9, Y66, Y103, Y124, Y169, Y172, Y173, F198, Y203, Y204, F251, W252) had no effect on substrate binding. The PhaZ7 wild-type protein, three muteins with single amino acid exchanges (Y105A, Y105E, Y190E), a PhaZ7 variant with deletion of residues 202-208, and PhaZ7 in which the active-site serine had been replaced by alanine (S136A) were crystallized and their structures were determined at 1.6-2.0 Å resolution. The structures were almost identical but revealed flexibility of some regions. Structural analysis of PhaZ7 (S136A) with bound 3-hydroxybutyrate tetramer showed that the substrate binds in a cleft that is composed of Y105, Y176, Y189 and Y190 and thus confirmed the data obtained by site-directed mutagenesis. To the best of our knowledge this is the first example in which the substrate binding site of a PHB depolymerase is documented at a molecular and structural level.

PubMed: 24007310
DOI: 10.1111/MMI.12391

Experimental method

X-RAY DIFFRACTION (1.598 Å)