Cited by 104biodegradable polymer synthesis and propertiesEnzyme Production and CharacterizationMicrobial bioremediation and biosurfactants

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Substrate and binding specificities of bacterial polyhydroxybutyrate depolymerases

Kasuya, Ken-ichi, Ohura, Takeshi, Masuda, Kozue, Doi, Yoshiharu·1999·International Journal of Biological Macromolecules

DOI 10.1016/s0141-8130(99)00046-x

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Abstract

The substrate specificities of three extracellular polyhydroxybutyrate (PHB) depolymerases from Alcaligenes faecalis (PhaZ Afa), Pseudomonas stutzeri (PhaZ Pst), and Comamonas acidovorans (PhaZ Cac), which are grouped into types A and B based on the position of a lipase box sequence in the catalytic domain, were examined for films of 12 different aliphatic polyesters. Each of these PHB depolymerases used was capable of hydrolyzing poly(3-hydroxybutyrate) (P(3HB)), poly(3-hydroxypropionate) (P(3HP)), poly(4-hydroxybutyrate) (P(4HB)), poly(ethylene succinate) (PESU), and poly(ethylene adipate) (PEA) but could not hydrolyze another seven polyesters. In addition, the binding characteristics of substrate binding domains from PhaZ Afa, PhaZ Cac, and PHB depolymerase from Comamonas testosteroni (PhaZ Cte) were studied by using fusions with glutathione S-transferase (GST). All of fusion proteins adsorbed strongly on the surfaces of polyester granules of P(3HB), P(3HP), and poly(2-hydroxypropionate) (P(2HP)) which was not hydrolyzed by the PHB depolymerases used in this study, while they did not bind on Avicel and chitin granules. The adsorption kinetics of the fusion proteins to the surface of P(3HB) and P(2HP) granules were found to obey the Langmuir isotherm. The cross-area per molecule of fusion protein bound to P(3HB) granules was estimated to be 12+/-4 nm2/molecule. It has been suggested that the active sites in catalytic domains of PHB depolymerases have a similar conformational structure, and that several amino acids in substrate-binding domains of PHB depolymerases interact specifically with the surface of polyesters.

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“…have a similar conformational structure, independently of a difference in the sequence structure of the catalytic domains given that they were able to degrade the same 5 substrates (PHB, PHP, P(4HB), poly(ethylene-succinate) and poly(ethylene-adipate)) and unable to degrade the other seven [180].”
SÍNTESIS Y BIODEGRADACIÓN DE POLIHIDROXIALCANOATOS: PLÁSTICOS DE ORIGEN MICROBIANO
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“…sp. RY-1 X Kim et al. (2000a,b) Pseudomonas indica K2 X Elbanna et al. (2004) Pseudomonas luteola M13-4 X Rhee et al. (2006) Ralstonia pickettii X Kasuya et al. (1999) Rhodospirillum rubrum X Reddy et al. (2003) Rhizobium (Sinorhizobium) meliloti Aneja y Charles, (1999) Streptomyces exfoliates…”
BackgroundInfluential
Changes in the Development and Reproductive Output of Nitokra lacustris pacifica (Crustacea: Copepoda) Yeatman, 1983 Under Short and Long Term Exposure to Synthetic and Biodegradable Microbeads
Jaapar, A. N., Amin, R. M., Bhubalan, K., & Sohaimi, E. S. (2021) · Journal of Polymers and the Environment · doi:10.1007/s10924-021-02165-8 · Cited by 18
“This variation in the degradation rate is due to surface morphology, the origin of microorganisms, and its total concentration in different environments as well as their ability to degrade each polymer [33, 78, 80, 81].”
Background
Characterization of a thermolabile poly(3-hydroxybutyrate) depolymerase from the marine bacterium Shewanella sp. JKCM-AJ-6,1α
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Purification and Properties of a Poly (β-hydroxybutyrate) Depolymerase From Penicillium sp.
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Micropatterning proteins on polyhydroxyalkanoate substrates by using the substrate binding domain as a fusion partner
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“of PHAs by recognizing the hydrophobic side chains and chemically interacting with it (Jendrossek and Handrick, 2002;Kasuya et al., 1999;Ohura et al., 1999;Yamashita et al., 2001).”
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Anchor peptides promote degradation of mixed plastics for recycling
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A Human Antibody Fragment with High Affinity for Biodegradable Polymer Film
Watanabe, H., Tsumoto, K., Taguchi, S., Yamashita, K., Doi, Y., Nishimiya, Y., Kondo, H., Umetsu, M., & Kumagai, I. (2007) · Bioconjugate Chemistry · doi:10.1021/bc060203y · Cited by 16
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Poly(hydroxyalkanoate)s
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Grafting of material-binding function into antibodies
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Ring‐Opening Polymerization Strategies for Degradable Polyesters
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Design of Plastic Binding Lytic Polysaccharide Monooxygenases via Modular Engineering
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Enzymatic Hydrolysis of Chemosynthesized Atactic Poly(3-hydroxybutyrate) by Poly(3-hydroxyalkanoate) Depolymerase from Acidovorax Sp. TP4 and Ralstonia pickettii T1
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Self-citation
Adsorption effects of poly(hydroxybutyric acid) depolymerase on chain-folding surface of polyester single crystals revealed by mutant enzyme and frictional force microscopy
Numata, K., Sato, S., Fujita, M., Tsuge, T., Iwata, T., Doi, Y., & Abe, H. (2006) · Polymer Degradation and Stability · doi:10.1016/j.polymdegradstab.2006.07.029 · Cited by 13
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Microarray of DNA–protein complexes on poly-3-hydroxybutyrate surface for pathogen detection
Park, T. J., Yoo, S. M., Keum, K. C., & Lee, S. Y. (2008) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-008-2574-y · Cited by 13
Protein Engineering of Enzymes Involved in Bioplastic Metabolism
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Molecular and Material Design of Biodegradable Polyhydroxyalkanoates (PHAs)
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Self-citation
Marine biodegradation mechanism of biodegradable plastics revealed by plastisphere analysisPreprint
Suzuki, M., Ishii, S., Gonda, K., Kashima, H., Suzuki, S., Uematsu, K., Arai, T., Tachibana, Y., Iwata, T., & Kasuya, K. (2022) · Research Square · doi:10.21203/rs.3.rs-2014166/v1 · Cited by 10
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Biodegradable poly(ethylene succinate) blends and copolymers containing minor amounts of poly(butylene succinate)
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A Novel Actinobacterial Cutinase Containing a Noncatalytic Polymer-Binding Domain
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“by dissolving the polymer in chloroform and precipitated by addition of methanol (52).”
BackgroundMethod
Surface oxidation of polyhydroxyalkanoate films with different molecular structure via photo-activated chlorine dioxide radical and comparison of the influence on the properties
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Co‐Expression of ORFCma with PHB Depolymerase (PhaZCma) in Escherichia coli Induces Efficient Whole‐Cell Biodegradation of Polyesters
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Biomimetic Engineering of Modular Bispecific Antibodies for Biomolecule Immobilization
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Natural Polyester‐Related Proteins: Structure, Function, Evolution and Engineering
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Polyethylene glycol grafting by thiol‐ene reaction for the chemical modification of polyhydroxyalkanoates
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The biodegradable poly(3-hydroxypropionate) from acrylic acid via 3-hydroxypropionic acid: Studies on catalytic hydration and self-polycondensation
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Functional characterization and domain shuffling of poly(3-hydroxybutyrate) depolymerases from Cupriavidus malaysiensis and Pseudomonas guguanensis for sustainable bioplastic degradation
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Plastic leachates alter the composition of marine microbial communities, not functional potential for plastic degradation
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Purification and Characterization of Poly(ethylene succinate) Hydrolase from the Mesophilic Fungus Aspergillus clavatus NKCM1003
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Design and synthesis of biodegradable thermoplastic polyurethanes for tissue engineering
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“Compared to known experimentally verified PHA depolymerases, SmPHBase is most similar to the PHB depolymerase from S. asco-mycinicus [72] and Comamonas acidovorans [87] with 71 and 56% identity, respectively.”
Assessing feasibility of promoting fertilizer utilization facilitated by controlled release of bacteria-encapsulated film bag
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Identification of an Extracellular Poly(3-hydroxybutyrate) Depolymerase in the Genus Alteromonas and Its Phylogenetic Distribution Among Alteromonas Species
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Unveiling plastic biodegradation pathways through 13C-DNA stable isotope probing and metagenomics
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Microbial Degradation of Polyhydroxyalkanoates in Fresh Tropical Water
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Structure and Hydrolysis of Polyester Single Crystals
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Self-citation

Authors: Kasuya, K.-I., Ohura, T., Masuda, K., & Doi, Y.
Affiliations: RIKEN (JP)
Saitama University (JP)
Corresponding author: Doi, Yoshiharu
ORCID: Kasuya, Ken-ichi
Ohura, Takeshi
Venue: International Journal of Biological Macromolecules
Publisher: Elsevier BV
Published: 1999-05
Volume: 24
Issue: 4
Pages: 329-336
ISSN: 0141-8130 (ISSN-L)
DOI: 10.1016/s0141-8130(99)00046-x
OpenAlex: W2027297590
Cited by: 104
References: 38
Citations by year: 2026: 3 · 2025: 9 · 2024: 5 · 2023: 7 · 2022: 5 · 2021: 5 · 2020: 4 · 2019: 3 · 2018: 1 · 2017: 4 · 2016: 4 · 2015: 3 · 2014: 1 · 2013: 2 · 2012: 3
FWCI: 4.43
Type: journal article
Language: en
Open access: closed
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
www.elsevier.com/legal/tdmrep-license (tdm)
Locations: International Journal of Biological Macromolecules (publishedVersion)
PubMed (publishedVersion)
Tokyo Tech Research Repository (Tokyo Institute of Technology) (submittedVersion)
Funders: Japan Science and Technology Corporation
Core Research for Evolutional Science and Technology
Topics: Physical Sciences › Materials Science › Biomaterials › biodegradable polymer synthesis and properties
Life Sciences › Biochemistry, Genetics and Molecular Biology › Biotechnology › Enzyme Production and Characterization
Physical Sciences › Environmental Science › Pollution › Microbial bioremediation and biosurfactants
Keywords: polyhydroxybutyrate depolymerase, substrate specificity, aliphatic polyesters, polyhydroxybutyrate, poly-4-hydroxybutyrate, poly(ethylene succinate), poly(ethylene adipate), substrate-binding domain, protein adsorption kinetics, Langmuir isotherm, Alcaligenes faecalis, Pseudomonas stutzeri, Comamonas acidovorans, Comamonas testosteroni, extracellular enzymes
MeSH terms: Polyhydroxybutyrates, Adsorption, Alcaligenes, Amino Acid Sequence, Binding Sites, Carboxylic Ester Hydrolases, Hydrolysis, Hydroxybutyrates, Molecular Sequence Data, Polyesters, Pseudomonas, Recombinant Fusion Proteins, Substrate Specificity, Gram-Negative Aerobic Rods and Cocci, Sequence Homology, Amino Acid

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Substrate and binding specificities of bacterial polyhydroxybutyrate depolymerases

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