Structural basis of poly(3-hydroxybutyrate) hydrolysis by PhaZ7 depolymerase from Paucimonas lemoignei

Journal of Molecular Biology
Anastassios C PapageorgiouDieter Jendrossek

Abstract

The crystal structure of poly(3-hydroxybutyrate) (PHB) depolymerase PhaZ7 purified from Paucimonas lemoignei was determined at 1.90 A resolution. The structure consists of a single domain with an alpha/beta hydrolase fold in its core. The active site is analogous to that of serine esterases/lipases and is characterized by the presence of a catalytic triad comprising Ser136, Asp242, and His306. Comparison with other structures in the Protein Data Bank showed a high level of similarity with the Bacillus subtilis lipase LipA (RMSD, 1.55 A). Structural comparison with Penicillium funiculosum PHB depolymerase, the only PHB depolymerase whose structure is already known, revealed significant differences, resulting in an RMSD of 2.80-3.58 A. The two enzymes appear to utilize different types of solvent-exposed residues for biopolymer binding, with aliphatic and hydroxyl residues used in P. funiculosum PHB depolymerase and aromatic residues in PhaZ7. Moreover, the active site of P. funiculosum PHB depolymerase is accessible to the substrate in contrast to the active site of PhaZ7, which is buried. Hence, considerable conformational changes are required in PhaZ7 for the creation of a channel leading to the active site. Taken together, the...Continue Reading

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Citations

Jun 3, 2010·Acta Crystallographica. Section F, Structural Biology and Crystallization Communications·Sachin WakadkarAnastassios C Papageorgiou
Jan 1, 2015·International Journal of Molecular Sciences·Joanna RydzDarinka Christova
May 25, 2013·Cell Calcium·Matthew SmithenEvgeny Pavlov
Aug 13, 2017·Applied and Environmental Microbiology·Dai KomiyaShinya Fushinobu
Oct 13, 2018·Protein Science : a Publication of the Protein Society·Polytimi S DimitriouKonstantin Denessiouk
Oct 8, 2014·Acta Crystallographica. Section F, Structural Biology Communications·Yung Lin WangShwu Huey Liaw
Jun 6, 2017·Molecular Biotechnology·Rauda A MohamedMohd Basyaruddin Abdul Rahman
Sep 26, 2016·Journal of Bioenergetics and Biomembranes·Pia A ElustondoEvgeny V Pavlov
Nov 20, 2019·Biochimica Et Biophysica Acta. Proteins and Proteomics·Aneta K UrbanekMiguel Arroyo

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