Poly(3-hydroxybutyrate) depolymerase

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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.

Contents

poly(3-hydroxybutyrate) depolymerase
Identifiers
EC no. 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
Search
PMC articles
PubMed articles
NCBI proteins

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]

Related Research Articles

<span class="mw-page-title-main">Polyhydroxybutyrate</span>

Polyhydroxybutyrate (PHB) is a polyhydroxyalkanoate (PHA), a polymer belonging to the polyesters class that are of interest as bio-derived and biodegradable plastics. The poly-3-hydroxybutyrate (P3HB) form of PHB is probably the most common type of polyhydroxyalkanoate, but other polymers of this class are produced by a variety of organisms: these include poly-4-hydroxybutyrate (P4HB), polyhydroxyvalerate (PHV), polyhydroxyhexanoate (PHH), polyhydroxyoctanoate (PHO) and their copolymers.

<span class="mw-page-title-main">Polyhydroxyalkanoates</span> Polyester family

Polyhydroxyalkanoates or PHAs are polyesters produced in nature by numerous microorganisms, including through bacterial fermentation of sugars or lipids. When produced by bacteria they serve as both a source of energy and as a carbon store. More than 150 different monomers can be combined within this family to give materials with extremely different properties. These plastics are biodegradable and are used in the production of bioplastics.

<i>Alcaligenes faecalis</i> Species of bacterium

Alcaligenes faecalis is a species of Gram-negative, rod-shaped bacteria commonly found in the environment. It was originally named for its first discovery in feces, but was later found to be common in soil, water, and environments in association with humans. While opportunistic infections do occur, the bacterium is generally considered nonpathogenic. When an opportunistic infection does occur, it is usually observed in the form of a urinary tract infection.

4-Hydroxybenzoic acid, also known as p-hydroxybenzoic acid (PHBA), is a monohydroxybenzoic acid, a phenolic derivative of benzoic acid. It is a white crystalline solid that is slightly soluble in water and chloroform but more soluble in polar organic solvents such as alcohols and acetone. 4-Hydroxybenzoic acid is primarily known as the basis for the preparation of its esters, known as parabens, which are used as preservatives in cosmetics and some ophthalmic solutions. It is isomeric with 2-hydroxybenzoic acid, known as salicylic acid, a precursor to aspirin, and with 3-hydroxybenzoic acid.

The indole test is a biochemical test performed on bacterial species to determine the ability of the organism to convert tryptophan into indole. This division is performed by a chain of a number of different intracellular enzymes, a system generally referred to as "tryptophanase."

β-Hydroxybutyric acid Chemical compound

β-Hydroxybutyric acid, also known as 3-hydroxybutyric acid or BHB, is an organic compound and a beta hydroxy acid with the chemical formula CH3CH(OH)CH2CO2H; its conjugate base is β-hydroxybutyrate, also known as 3-hydroxybutyrate. β-Hydroxybutyric acid is a chiral compound with two enantiomers: D-β-hydroxybutyric acid and L-β-hydroxybutyric acid. Its oxidized and polymeric derivatives occur widely in nature. In humans, D-β-hydroxybutyric acid is one of two primary endogenous agonists of hydroxycarboxylic acid receptor 2 (HCA2), a Gi/o-coupled G protein-coupled receptor (GPCR).

<span class="mw-page-title-main">Biodegradable plastic</span> Plastics that can be decomposed by the action of living organisms

Biodegradable plastics are plastics that can be decomposed by the action of living organisms, usually microbes, into water, carbon dioxide, and biomass. Biodegradable plastics are commonly produced with renewable raw materials, micro-organisms, petrochemicals, or combinations of all three.

Paucimonas lemoignei, formerly [Pseudomonas lemoignei], is a Gram-negative soil bacterium. It is aerobic, motile, and rod-shaped.

In enzymology, 3-hydroxybutyrate dehydrogenase (EC 1.1.1.30) is an enzyme that catalyzes the chemical reaction:

<span class="mw-page-title-main">Maleate isomerase</span>

In enzymology, a maleate isomerase, or maleate cis-tran isomerase, is a member of the Asp/Glu racemase superfamily discovered in bacteria. It is responsible for catalyzing cis-trans isomerization of the C2-C3 double bond in maleate to produce fumarate, which is a critical intermediate in citric acid cycle. The presence of an exogenous mercaptan is required for catalysis to happen.

<span class="mw-page-title-main">Biodegradable polymer</span>

Biodegradable polymers are a special class of polymer that breaks down after its intended purpose by bacterial decomposition process to result in natural byproducts such as gases (CO2, N2), water, biomass, and inorganic salts. These polymers are found both naturally and synthetically made, and largely consist of ester, amide, and ether functional groups. Their properties and breakdown mechanism are determined by their exact structure. These polymers are often synthesized by condensation reactions, ring opening polymerization, and metal catalysts. There are vast examples and applications of biodegradable polymers.

The enzyme hydroxybutyrate-dimer hydrolase (EC 3.1.1.22) catalyzes the reaction

The enzyme poly(3-hydroxyoctanoate) depolymerase (EC 3.1.1.76) catalyzes the hydrolysis of the polyester poly{oxycarbonyl[(R)-2-pentylethylene] to oligomers

In enzymology, a mandelamide amidase (EC 3.5.1.86) is an enzyme that catalyzes the chemical reaction

Streptomyces exfoliatus is a bacterium species from the genus of Streptomyces which has been isolated from soil. Streptomyces exfoliatus has the ability to degrade poly(3-hydroxyalkanoate). This species produces exfoliatin and exfoliamycin.

Nocardiopsis aegyptia is a Gram-positive and aerobic bacterium from the genus of Nocardiopsis which has been isolated from marine sediments from the Abu Qir Bay from Alexandria in Egypt. Nocardiopsis aegyptia can degrade poly(3-hydroxybutyrate) (PHB).

<span class="mw-page-title-main">PETase</span> Class of enzymes

PETases are an esterase class of enzymes that catalyze the breakdown (via hydrolysis) of polyethylene terephthalate (PET) plastic to monomeric mono-2-hydroxyethyl terephthalate (MHET). The idealized chemical reaction is:

β-Butyrolactone Chemical compound

β-Butyrolactone is the intramolecular carboxylic acid ester (lactone) of the optically active 3-hydroxybutanoic acid. It is produced during chemical synthesis as a racemate. β-Butyrolactone is suitable as a monomer for the production of the biodegradable polyhydroxyalkanoate poly(3-hydroxybutyrate) (PHB). Polymerisation of racemic (RS)-β-butyrolactone provides (RS)-polyhydroxybutyric acid, which, however, is inferior in essential properties (e.g. strength or degradation behaviour) to the (R)-poly-3-hydroxybutyrate originating from natural sources.

<span class="mw-page-title-main">Plastic degradation by marine bacteria</span> Ability of bacteria to break down plastic polymers

Plastic degradation in marine bacteria describes when certain pelagic bacteria break down polymers and use them as a primary source of carbon for energy. Polymers such as polyethylene(PE), polypropylene (PP), and polyethylene terephthalate (PET) are incredibly useful for their durability and relatively low cost of production, however it is their persistence and difficulty to be properly disposed of that is leading to pollution of the environment and disruption of natural processes. It is estimated that each year there are 9-14 million metric tons of plastic that are entering the ocean due to inefficient solutions for their disposal. The biochemical pathways that allow for certain microbes to break down these polymers into less harmful byproducts has been a topic of study to develop a suitable anti-pollutant.

An oleaginous microorganism is a type of microbe that accumulates lipid as a normal part of its metabolism. Oleaginous microbes may accumulate an array of different lipid compounds, including polyhydroxyalkanoates, triacylglycerols, and wax esters. Various microorganisms, including bacteria, fungi, and yeast, are known to accumulate lipids. These organisms are often researched for their potential use in producing fuels from waste products.

References

  1. ↑ Shirakura, Y; Fukui, T; Saito, T; Okamoto, Y; Narikawa, T; Koide, K; Tomita, K; Takemasa, T; Masamune, S (1986-01-15). "Degradation of poly(3-hydroxybutyrate) by poly(3-hydroxybutyrate) depolymerase from Alcaligenes faecalis T1". Biochimica et Biophysica Acta (BBA) - General Subjects. 880 (1): 46–53. doi:10.1016/0304-4165(86)90118-2. PMID   3942778.
  2. ↑ Tokiwa, Yutaka; Calabia, Buenaventurada; Ugwu, Charles; Aiba, Seiichi (2009-08-26). "Biodegradability of Plastics". International Journal of Molecular Sciences. 10 (9): 3722–3742. doi: 10.3390/ijms10093722 . ISSN   1422-0067. PMC   2769161 . PMID   19865515.
  3. 1 2 Kita, K; Ishimaru, K; Teraoka, M; Yanase, H; Kato, N (1995). "Properties of poly(3-hydroxybutyrate) depolymerase from a marine bacterium, Alcaligenes faecalis AE122". Applied and Environmental Microbiology. 61 (5): 1727–1730. Bibcode:1995ApEnM..61.1727K. doi:10.1128/AEM.61.5.1727-1730.1995. ISSN   0099-2240. PMC   167434 . PMID   7646009.
  4. 1 2 Jendrossek, Dieter (2001), Babel, Wolfgang; Steinbüchel, Alexander (eds.), "Microbial Degradation of Polyesters", Biopolyesters, Advances in Biochemical Engineering/Biotechnology, Berlin, Heidelberg: Springer Berlin Heidelberg, vol. 71, pp. 293–325, doi:10.1007/3-540-40021-4_10, ISBN   978-3-540-41141-3, PMID   11217416 , retrieved 2020-10-22
  5. ↑ 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". PLOS ONE. 15 (1): e0220095. Bibcode:2020PLoSO..1520095S. doi: 10.1371/journal.pone.0220095 . ISSN   1932-6203. PMC   6946144 . PMID   31910206.
  6. 1 2 3 4 5 Hisano, Tamao; Kasuya, Ken-ichi; Tezuka, Yoko; Ishii, Nariaki; Kobayashi, Teruyuki; Shiraki, Mari; Oroudjev, Emin; Hansma, Helen; Iwata, Tadahisa; Doi, Yoshiharu; Saito, Terumi (March 2006). "The Crystal Structure of Polyhydroxybutyrate Depolymerase from Penicillium funiculosum Provides Insights into the Recognition and Degradation of Biopolyesters". Journal of Molecular Biology. 356 (4): 993–1004. doi:10.1016/j.jmb.2005.12.028. PMID   16405909.
  7. ↑ 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)". Macromolecules. 29 (7): 2472–2478. Bibcode:1996MaMol..29.2472H. doi:10.1021/ma951361f. ISSN   0024-9297.
  8. ↑ 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". 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.
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