Biology:Poly(3-hydroxybutyrate) depolymerase
Poly(3-hydroxybutyrate) depolymerase (EC 3.1.1.75, PHB depolymerase, systematic name poly[(R)-3-hydroxybutanoate] hydrolase) is an enzyme used in the degradation processes of a natural polyester poly(3-hydroxyburate).[1] This enzyme has growing commercialization interests due to it implications in biodegradable plastic decomposition.
| poly(3-hydroxybutyrate) depolymerase | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||
| EC number | 3.1.1.75 | ||||||||
| Databases | |||||||||
| IntEnz | IntEnz view | ||||||||
| BRENDA | BRENDA entry | ||||||||
| ExPASy | NiceZyme view | ||||||||
| KEGG | KEGG entry | ||||||||
| MetaCyc | metabolic pathway | ||||||||
| PRIAM | profile | ||||||||
| PDB structures | RCSB PDB PDBe PDBsum | ||||||||
| Gene Ontology | AmiGO / QuickGO | ||||||||
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It catalyzes the reaction
- [(R)-3-hydroxybutanoate]n + H2O = [(R)-3-hydroxybutanoate]n-x + [(R)-3-hydroxybutanoate]x; x = 1–5
Other names in common use include PHB depolymerase, poly(3HB) depolymerase, poly[(R)-hydroxyalkanoic acid] depolymerase, poly(HA) depolymerase, poly(HASCL) depolymerase, and poly[(R)-3-hydroxybutyrate] hydrolase.
Function
This enzyme is used in a multitude of bacteria and microbes and anaerobic and aerobic environments. Species such as Pseudomonas lemoigne, Comamonas sp. Acidovorax faecalis, Aspergillus fumigatus and Variovorax paradoxus have been found in soil, Alcaligenes faecalis, Pseudomonas, Illyobacter delafieldi, have been found in aerobic sludge, and finally, Comamonas testosterone, Pseudomonas stutzeri, are found in seawater and lakewater.[2]
Among the most studied, Alcaligenes faecalis, uses this depolymerase to metabolize poly(3-hydroxybutyrate), breaking it down for its stores of carbon.[3] The metabolization of poly(3-hydroxybutyrate) allows for high growth rates in these organisms when the bioavailability of carbon in the environment is low.[4] Some of these microbes such as Alcaligenes faecalis AE122, can utilize this reaction to attain its sole source of carbon.[3]
As many studies focus on extracellular poly(3-hydroxybutyrate) depolymerase, there are both an intracellular and extracellular PHB depolymerase. Both intracellular and extracellular depolymerase function to break the ester bonds in PHB and produce water soluble products: PHB dimer and 3HB monomer.[5] Extracellular depolymerases are able to degrade upon partially denatured PHB molecules, whereas intracellular depolymerases act upon the native PHB molecule.[6]
Structure and Active Site
As of late 2007, two structures have been solved for this class of enzymes, with PDB accession codes 2D80 and 2D81.
The shape of poly(3-hydroxybutyrate) depolymerase is globular, consisting of a single domain, and is a circularly permuted variation of the α-β hydrolase fold.[6]
The amino acid residues of Ser39, Asp121, and His155, are found after the first (β1), third (β3), and fourth (β4) β-strands of the depolymerase.[6] The substrate binding site has at least 3 subsites in which monomer units of polyester substrates can bind.[6] Thirteen hydrophobic residues are aligned and exposed to solvent along the surface of the depolymerase and potentially allow for sufficient binding affinity without a distinct substrate-binding domain, this domain serves as the polymer-absorption site.[6]
The degradation of poly(3-hydroxyburate) is caused by splintering of the crystalline structure through surface erosion, thus allowing for an edge attack from the enzyme to hydrolyze the molecule into its products.[4] In a study on the degradation of single crystals of PHB it was found that PHB depolymerase, preferentially degrades the crystalline edges rather than the chain folds of the PHB molecule.[7][8]
References
- ↑ Shirakura, Y; Fukui, T; Saito, T; Okamoto, Y; Narikawa, T; Koide, K; Tomita, K; Takemasa, T et al. (1986-01-15). "Degradation of poly(3-hydroxybutyrate) by poly(3-hydroxybutyrate) depolymerase from Alcaligenes faecalis T1" (in en). Biochimica et Biophysica Acta (BBA) - General Subjects 880 (1): 46–53. doi:10.1016/0304-4165(86)90118-2. PMID 3942778. https://linkinghub.elsevier.com/retrieve/pii/0304416586901182.
- ↑ Tokiwa, Yutaka; Calabia, Buenaventurada; Ugwu, Charles; Aiba, Seiichi (2009-08-26). "Biodegradability of Plastics" (in en). International Journal of Molecular Sciences 10 (9): 3722–3742. doi:10.3390/ijms10093722. ISSN 1422-0067. PMID 19865515.
- ↑ 3.0 3.1 Kita, K; Ishimaru, K; Teraoka, M; Yanase, H; Kato, N (1995). "Properties of poly(3-hydroxybutyrate) depolymerase from a marine bacterium, Alcaligenes faecalis AE122." (in en). Applied and Environmental Microbiology 61 (5): 1727–1730. doi:10.1128/AEM.61.5.1727-1730.1995. ISSN 0099-2240. PMID 7646009. Bibcode: 1995ApEnM..61.1727K.
- ↑ 4.0 4.1 Jendrossek, Dieter (2001), Babel, Wolfgang; Steinbüchel, Alexander, eds., "Microbial Degradation of Polyesters", Biopolyesters, Advances in Biochemical Engineering/Biotechnology (Berlin, Heidelberg: Springer Berlin Heidelberg) 71: pp. 293–325, doi:10.1007/3-540-40021-4_10, ISBN 978-3-540-41141-3, PMID 11217416, http://link.springer.com/10.1007/3-540-40021-4_10, retrieved 2020-10-22
- ↑ Sayyed, R. Z.; Wani, S. J.; Alarfaj, Abdullah A.; Syed, Asad; El-Enshasy, Hesham Ali (2020-01-07). Kumar, Pradeep. ed. "Production, purification and evaluation of biodegradation potential of PHB depolymerase of Stenotrophomonas sp. RZS7" (in en). PLOS ONE 15 (1): e0220095. doi:10.1371/journal.pone.0220095. ISSN 1932-6203. PMID 31910206. Bibcode: 2020PLoSO..1520095S.
- ↑ 6.0 6.1 6.2 6.3 6.4 Hisano, Tamao; Kasuya, Ken-ichi; Tezuka, Yoko; Ishii, Nariaki; Kobayashi, Teruyuki; Shiraki, Mari; Oroudjev, Emin; Hansma, Helen et al. (March 2006). "The Crystal Structure of Polyhydroxybutyrate Depolymerase from Penicillium funiculosum Provides Insights into the Recognition and Degradation of Biopolyesters" (in en). Journal of Molecular Biology 356 (4): 993–1004. doi:10.1016/j.jmb.2005.12.028. PMID 16405909. https://linkinghub.elsevier.com/retrieve/pii/S0022283605015901.
- ↑ Hocking, Philippa J.; Marchessault, Robert H.; Timmins, Mark R.; Lenz, Robert W.; Fuller, R. Clinton (January 1996). "Enzymatic Degradation of Single Crystals of Bacterial and Synthetic Poly(β-hydroxybutyrate)" (in en). Macromolecules 29 (7): 2472–2478. doi:10.1021/ma951361f. ISSN 0024-9297. Bibcode: 1996MaMol..29.2472H. https://pubs.acs.org/doi/10.1021/ma951361f.
- ↑ Iwata, Tadahisa; Shiromo, Masakatsu; Doi, Yoshiharu (2002). "Surface structures of poly[(R)-3-hydroxybutyrate and its copolymer single crystals before and after enzymatic degradation with an extracellular PHB depolymerase"] (in en). Macromolecular Chemistry and Physics 203 (10–11): 1309–1316. doi:10.1002/1521-3935(200207)203:10/11<1309::AID-MACP1309>3.0.CO;2-P. ISSN 1521-3935. https://onlinelibrary.wiley.com/doi/abs/10.1002/1521-3935%28200207%29203%3A10/11%3C1309%3A%3AAID-MACP1309%3E3.0.CO%3B2-P.
- Jendrossek D (2001). "Microbial degradation of polyesters". Adv. Biochem. Eng. Biotechnol.. Advances in Biochemical Engineering/Biotechnology 71: 293–325. doi:10.1007/3-540-40021-4_10. ISBN 978-3-540-41141-3. PMID 11217416.
- "Novel biodegradable aromatic plastics from a bacterial source Genetic and biochemical studies on a route of the phenylacetyl-coa catabolon". J. Biol. Chem. 274 (41): 29228–41. 1999. doi:10.1074/jbc.274.41.29228. PMID 10506180.
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