Sandbox Reserved 1643 - Revision history

Clara Felice at 20:33, 19 January 2022

Clara Felice — Wed, 19 Jan 2022 20:33:39 GMT

←Older revision		Revision as of 20:33, 19 January 2022
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	== PET Hydrolase ==		== PET Hydrolase ==
	<StructureSection load='6ane' size='340' side='right' caption='PET Hydrolase assymetric unit' scene=''>		<StructureSection load='6ane' size='340' side='right' caption='PET Hydrolase assymetric unit' scene=''>
-	PET hydrolase (also known as PETase) is an enzyme isolated from the bacteria Ideonella sakaiensis <ref name="discovery I. saka">DOI: 10.1126/science.aad6359</ref>. It is a type of enzyme called esterase that belongs to the α/β-hydrolase superfamily (EC 3.1.1.101.) <ref> BRENDA:EC3.1.1.101 ; Information on EC 3.1.1.101 - poly(ethylene terephthalate) hydrolase ; https://www.brenda-enzymes.org/enzyme.php?ecno=3.1.1.101 </ref>.	+	PET hydrolase (also known as PETase) is a trimer enzyme isolated from the bacteria Ideonella sakaiensis <ref name="discovery I. saka">DOI: 10.1126/science.aad6359</ref>. It is a type of enzyme called esterase that belongs to the α/β-hydrolase superfamily (EC 3.1.1.101.) <ref> BRENDA:EC3.1.1.101 ; Information on EC 3.1.1.101 - poly(ethylene terephthalate) hydrolase ; https://www.brenda-enzymes.org/enzyme.php?ecno=3.1.1.101 </ref>.
	It was in 2016, that Yoshida et al. discovered the bacterium Ideonella sakaiensis 201-F6 <ref name="discovery I. saka" />. The enzyme PETase allows this bacterium to grow by degrading PET (Polyethylene Terephthalate) that is used as its main carbon and energy source.		It was in 2016, that Yoshida et al. discovered the bacterium Ideonella sakaiensis 201-F6 <ref name="discovery I. saka" />. The enzyme PETase allows this bacterium to grow by degrading PET (Polyethylene Terephthalate) that is used as its main carbon and energy source.

Clara Felice at 20:29, 19 January 2022

Clara Felice — Wed, 19 Jan 2022 20:29:29 GMT

←Older revision		Revision as of 20:29, 19 January 2022
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	==== '''Catalytic site''' ====		==== '''Catalytic site''' ====

-	The PETase discovered in I. sakaiensis is a cutinase-like serine hydrolase. As in every cutinase, the catalytic site is made of a serine, a histidine and an aspartate. Altogether, they are called the catalytic triad. In PETase, these three amino acids are <scene name='86/868176/Catalytic_triad/1'>S133, H210 and D179</scene> <ref name="structure">DOI:10.1016/j.bpj.2018.02.005</ref>. The PETase follows the canonical serine hydrolase catalytic mechanism when PET binds to the enzyme. The serine performs a nucleophilic attack on the substrate, then the basic amino acid histidine polarizes the serine and the acidic amino acid aspartate stabilizes the histidine <ref name="current and futur perspectives">DOI:10.3389/fmicb.2020.571265</ref>. The reaction mechanism takes place in two steps, acylation and deacylation. Acylation consists of proton transfer from Ser133 to His210 and a nucleophilic attack by Ser133 on the substrate, leading to a tetrahedral transition state. Deacylation consists of deprotonation of a water molecule by His210, resulting in a hydroxide attacking the acylated Ser133 intermediate and breaking its bond to the substrate. His210 transfers the water’s proton to Ser133, with formation of MHET and enzyme regeneration <ref> Reaction Mechanism of the PET Degrading Enzyme PETase Studied with DFT/MM Molecular Dynamics Simulations. Carola Jerves, Rui P. P. Neves, Maria J. Ramos, Maria J. Ramos, Saulo da Silva, and Pedro A. Fernandes. ACS Catal. 2021, 11, 18, 11626–11638 . Publication Date:September 3, 2021. https://doi.org/10.1021/acscatal.1c03700 </ref>.	+	The PETase discovered in I. sakaiensis is a cutinase-like serine hydrolase. As in every cutinase, the catalytic site is made of a serine, a histidine and an aspartate. Altogether, they are called the catalytic triad. In PETase, these three amino acids are <scene name='86/868176/Catalytic_triad/2'>S133, H210 and D179</scene> <ref name="structure">DOI:10.1016/j.bpj.2018.02.005</ref>. The PETase follows the canonical serine hydrolase catalytic mechanism when PET binds to the enzyme. The serine performs a nucleophilic attack on the substrate, then the basic amino acid histidine polarizes the serine and the acidic amino acid aspartate stabilizes the histidine <ref name="current and futur perspectives">DOI:10.3389/fmicb.2020.571265</ref>. The reaction mechanism takes place in two steps, acylation and deacylation. Acylation consists of proton transfer from Ser133 to His210 and a nucleophilic attack by Ser133 on the substrate, leading to a tetrahedral transition state. Deacylation consists of deprotonation of a water molecule by His210, resulting in a hydroxide attacking the acylated Ser133 intermediate and breaking its bond to the substrate. His210 transfers the water’s proton to Ser133, with formation of MHET and enzyme regeneration <ref> Reaction Mechanism of the PET Degrading Enzyme PETase Studied with DFT/MM Molecular Dynamics Simulations. Carola Jerves, Rui P. P. Neves, Maria J. Ramos, Maria J. Ramos, Saulo da Silva, and Pedro A. Fernandes. ACS Catal. 2021, 11, 18, 11626–11638 . Publication Date:September 3, 2021. https://doi.org/10.1021/acscatal.1c03700 </ref>.
	Questions remain regarding the mobility of certain residues during the catalytic cycle.		Questions remain regarding the mobility of certain residues during the catalytic cycle.

Clara Felice at 20:21, 19 January 2022

Clara Felice — Wed, 19 Jan 2022 20:21:20 GMT

←Older revision		Revision as of 20:21, 19 January 2022
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	==== '''Catalytic site''' ====		==== '''Catalytic site''' ====

-	The PETase discovered in I. sakaiensis is a cutinase-like serine hydrolase. As in every cutinase, the catalytic site is made of a serine, a histidine and an aspartate. Altogether, they are called the catalytic triad. In PETase, these three amino acids are <scene name='86/868176/~~Petase_catalytictriad_ba1~~/1'>S133, H210 and D179</scene> <ref name="structure">DOI:10.1016/j.bpj.2018.02.005</ref>. The PETase follows the canonical serine hydrolase catalytic mechanism when PET binds to the enzyme. The serine performs a nucleophilic attack on the substrate, then the basic amino acid histidine polarizes the serine and the acidic amino acid aspartate stabilizes the histidine <ref name="current and futur perspectives">DOI:10.3389/fmicb.2020.571265</ref>. The reaction mechanism takes place in two steps, acylation and deacylation. Acylation consists of proton transfer from Ser133 to His210 and a nucleophilic attack by Ser133 on the substrate, leading to a tetrahedral transition state. Deacylation consists of deprotonation of a water molecule by His210, resulting in a hydroxide attacking the acylated Ser133 intermediate and breaking its bond to the substrate. His210 transfers the water’s proton to Ser133, with formation of MHET and enzyme regeneration <ref> Reaction Mechanism of the PET Degrading Enzyme PETase Studied with DFT/MM Molecular Dynamics Simulations. Carola Jerves, Rui P. P. Neves, Maria J. Ramos, Maria J. Ramos, Saulo da Silva, and Pedro A. Fernandes. ACS Catal. 2021, 11, 18, 11626–11638 . Publication Date:September 3, 2021. https://doi.org/10.1021/acscatal.1c03700 </ref>.	+	The PETase discovered in I. sakaiensis is a cutinase-like serine hydrolase. As in every cutinase, the catalytic site is made of a serine, a histidine and an aspartate. Altogether, they are called the catalytic triad. In PETase, these three amino acids are <scene name='86/868176/Catalytic_triad/1'>S133, H210 and D179</scene> <ref name="structure">DOI:10.1016/j.bpj.2018.02.005</ref>. The PETase follows the canonical serine hydrolase catalytic mechanism when PET binds to the enzyme. The serine performs a nucleophilic attack on the substrate, then the basic amino acid histidine polarizes the serine and the acidic amino acid aspartate stabilizes the histidine <ref name="current and futur perspectives">DOI:10.3389/fmicb.2020.571265</ref>. The reaction mechanism takes place in two steps, acylation and deacylation. Acylation consists of proton transfer from Ser133 to His210 and a nucleophilic attack by Ser133 on the substrate, leading to a tetrahedral transition state. Deacylation consists of deprotonation of a water molecule by His210, resulting in a hydroxide attacking the acylated Ser133 intermediate and breaking its bond to the substrate. His210 transfers the water’s proton to Ser133, with formation of MHET and enzyme regeneration <ref> Reaction Mechanism of the PET Degrading Enzyme PETase Studied with DFT/MM Molecular Dynamics Simulations. Carola Jerves, Rui P. P. Neves, Maria J. Ramos, Maria J. Ramos, Saulo da Silva, and Pedro A. Fernandes. ACS Catal. 2021, 11, 18, 11626–11638 . Publication Date:September 3, 2021. https://doi.org/10.1021/acscatal.1c03700 </ref>.
	Questions remain regarding the mobility of certain residues during the catalytic cycle.		Questions remain regarding the mobility of certain residues during the catalytic cycle.

Clara Felice at 19:20, 19 January 2022

Clara Felice — Wed, 19 Jan 2022 19:20:41 GMT

←Older revision		Revision as of 19:20, 19 January 2022
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-
	== PET Hydrolase ==		== PET Hydrolase ==
	<StructureSection load='6ane' size='340' side='right' caption='PET Hydrolase assymetric unit' scene=''>		<StructureSection load='6ane' size='340' side='right' caption='PET Hydrolase assymetric unit' scene=''>

Clara Felice at 14:37, 19 January 2022

Clara Felice — Wed, 19 Jan 2022 14:37:58 GMT

←Older revision		Revision as of 14:37, 19 January 2022
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-	<Structure load='Insert PDB code or filename here' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />{{Sandbox_Reserved_ESBS20_}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->	+
	== PET Hydrolase ==		== PET Hydrolase ==
	<StructureSection load='6ane' size='340' side='right' caption='PET Hydrolase assymetric unit' scene=''>		<StructureSection load='6ane' size='340' side='right' caption='PET Hydrolase assymetric unit' scene=''>

Clara Felice at 14:37, 19 January 2022

Clara Felice — Wed, 19 Jan 2022 14:37:30 GMT

←Older revision		Revision as of 14:37, 19 January 2022
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-	{{Sandbox_Reserved_ESBS20_}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->	+	<Structure load='Insert PDB code or filename here' size='350' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />{{Sandbox_Reserved_ESBS20_}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
	== PET Hydrolase ==		== PET Hydrolase ==
	<StructureSection load='6ane' size='340' side='right' caption='PET Hydrolase assymetric unit' scene=''>		<StructureSection load='6ane' size='340' side='right' caption='PET Hydrolase assymetric unit' scene=''>

Clara Felice at 22:34, 18 January 2022

Clara Felice — Tue, 18 Jan 2022 22:34:58 GMT

←Older revision		Revision as of 22:34, 18 January 2022
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	==== '''Catalytic site''' ====		==== '''Catalytic site''' ====

-	The PETase discovered in I. sakaiensis is a cutinase-like serine hydrolase. As in every cutinase, the catalytic site is made of ~~<scene name='86/868176/Petase_catalytictriad_ba1/1'>~~a serine, a histidine and an aspartate~~</scene>~~. Altogether, they are called the catalytic triad. In PETase, these three amino acids are S133, H210 and D179 <ref name="structure">DOI:10.1016/j.bpj.2018.02.005</ref>. The PETase follows the canonical serine hydrolase catalytic mechanism when PET binds to the enzyme. The serine performs a nucleophilic attack on the substrate, then the basic amino acid histidine polarizes the serine and the acidic amino acid aspartate stabilizes the histidine <ref name="current and futur perspectives">DOI:10.3389/fmicb.2020.571265</ref>. The reaction mechanism takes place in two steps, acylation and deacylation. Acylation consists of proton transfer from Ser133 to His210 and a nucleophilic attack by Ser133 on the substrate, leading to a tetrahedral transition state. Deacylation consists of deprotonation of a water molecule by His210, resulting in a hydroxide attacking the acylated Ser133 intermediate and breaking its bond to the substrate. His210 transfers the water’s proton to Ser133, with formation of MHET and enzyme regeneration <ref> Reaction Mechanism of the PET Degrading Enzyme PETase Studied with DFT/MM Molecular Dynamics Simulations. Carola Jerves, Rui P. P. Neves, Maria J. Ramos, Maria J. Ramos, Saulo da Silva, and Pedro A. Fernandes. ACS Catal. 2021, 11, 18, 11626–11638 . Publication Date:September 3, 2021. https://doi.org/10.1021/acscatal.1c03700 </ref>.	+	The PETase discovered in I. sakaiensis is a cutinase-like serine hydrolase. As in every cutinase, the catalytic site is made of a serine, a histidine and an aspartate. Altogether, they are called the catalytic triad. In PETase, these three amino acids are <scene name='86/868176/Petase_catalytictriad_ba1/1'>S133, H210 and D179</scene> <ref name="structure">DOI:10.1016/j.bpj.2018.02.005</ref>. The PETase follows the canonical serine hydrolase catalytic mechanism when PET binds to the enzyme. The serine performs a nucleophilic attack on the substrate, then the basic amino acid histidine polarizes the serine and the acidic amino acid aspartate stabilizes the histidine <ref name="current and futur perspectives">DOI:10.3389/fmicb.2020.571265</ref>. The reaction mechanism takes place in two steps, acylation and deacylation. Acylation consists of proton transfer from Ser133 to His210 and a nucleophilic attack by Ser133 on the substrate, leading to a tetrahedral transition state. Deacylation consists of deprotonation of a water molecule by His210, resulting in a hydroxide attacking the acylated Ser133 intermediate and breaking its bond to the substrate. His210 transfers the water’s proton to Ser133, with formation of MHET and enzyme regeneration <ref> Reaction Mechanism of the PET Degrading Enzyme PETase Studied with DFT/MM Molecular Dynamics Simulations. Carola Jerves, Rui P. P. Neves, Maria J. Ramos, Maria J. Ramos, Saulo da Silva, and Pedro A. Fernandes. ACS Catal. 2021, 11, 18, 11626–11638 . Publication Date:September 3, 2021. https://doi.org/10.1021/acscatal.1c03700 </ref>.
	Questions remain regarding the mobility of certain residues during the catalytic cycle.		Questions remain regarding the mobility of certain residues during the catalytic cycle.

Clara Felice at 22:30, 18 January 2022

Clara Felice — Tue, 18 Jan 2022 22:30:53 GMT

←Older revision		Revision as of 22:30, 18 January 2022
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	==== '''Catalytic site''' ====		==== '''Catalytic site''' ====

-	The PETase discovered in I. sakaiensis is a cutinase-like serine hydrolase. As in every cutinase, the catalytic site is made of <scene name='86/868176/Petase_catalytictriad_ba1/1'>a serine, a histidine and an aspartate</scene>. Altogether, they are called the catalytic triad. In PETase, these three amino acids are S133, H210 and D179 <ref name="structure">DOI:10.1016/j.bpj.2018.02.005</ref>. The PETase follows the canonical serine hydrolase catalytic mechanism when PET binds to the enzyme. The serine performs a nucleophilic attack on the substrate, then the basic amino acid histidine polarizes the serine and the acidic amino acid aspartate stabilizes the histidine <ref name="current and futur perspectives">DOI:10.3389/fmicb.2020.571265</ref>. The reaction mechanism takes place in two steps, acylation and deacylation. Acylation consists of proton transfer from Ser133 to His210 and a nucleophilic attack by Ser133 on the substrate, leading to a tetrahedral transition state. Deacylation consists of deprotonation of a water molecule by His210, resulting in a hydroxide attacking the acylated Ser133 intermediate and breaking its bond to the substrate. His210 transfers the water’s proton to Ser133, with formation of MHET and enzyme regeneration. ~~[???]~~	+	The PETase discovered in I. sakaiensis is a cutinase-like serine hydrolase. As in every cutinase, the catalytic site is made of <scene name='86/868176/Petase_catalytictriad_ba1/1'>a serine, a histidine and an aspartate</scene>. Altogether, they are called the catalytic triad. In PETase, these three amino acids are S133, H210 and D179 <ref name="structure">DOI:10.1016/j.bpj.2018.02.005</ref>. The PETase follows the canonical serine hydrolase catalytic mechanism when PET binds to the enzyme. The serine performs a nucleophilic attack on the substrate, then the basic amino acid histidine polarizes the serine and the acidic amino acid aspartate stabilizes the histidine <ref name="current and futur perspectives">DOI:10.3389/fmicb.2020.571265</ref>. The reaction mechanism takes place in two steps, acylation and deacylation. Acylation consists of proton transfer from Ser133 to His210 and a nucleophilic attack by Ser133 on the substrate, leading to a tetrahedral transition state. Deacylation consists of deprotonation of a water molecule by His210, resulting in a hydroxide attacking the acylated Ser133 intermediate and breaking its bond to the substrate. His210 transfers the water’s proton to Ser133, with formation of MHET and enzyme regeneration <ref> Reaction Mechanism of the PET Degrading Enzyme PETase Studied with DFT/MM Molecular Dynamics Simulations. Carola Jerves, Rui P. P. Neves, Maria J. Ramos, Maria J. Ramos, Saulo da Silva, and Pedro A. Fernandes. ACS Catal. 2021, 11, 18, 11626–11638 . Publication Date:September 3, 2021. https://doi.org/10.1021/acscatal.1c03700 </ref>.
	Questions remain regarding the mobility of certain residues during the catalytic cycle.		Questions remain regarding the mobility of certain residues during the catalytic cycle.

Clara Felice at 22:29, 18 January 2022

Clara Felice — Tue, 18 Jan 2022 22:29:38 GMT

←Older revision		Revision as of 22:29, 18 January 2022
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	== PET Hydrolase ==		== PET Hydrolase ==
	<StructureSection load='6ane' size='340' side='right' caption='PET Hydrolase assymetric unit' scene=''>		<StructureSection load='6ane' size='340' side='right' caption='PET Hydrolase assymetric unit' scene=''>
-	PET hydrolase (also known as PETase) is an enzyme isolated from the bacteria Ideonella sakaiensis <ref name="discovery I. saka">DOI: 10.1126/science.aad6359</ref>. It is a type of enzyme called esterase that belongs to the α/β-hydrolase superfamily (EC 3.1.1.101.) [?].	+	PET hydrolase (also known as PETase) is an enzyme isolated from the bacteria Ideonella sakaiensis <ref name="discovery I. saka">DOI: 10.1126/science.aad6359</ref>. It is a type of enzyme called esterase that belongs to the α/β-hydrolase superfamily (EC 3.1.1.101.) <ref> BRENDA:EC3.1.1.101 ; Information on EC 3.1.1.101 - poly(ethylene terephthalate) hydrolase ; https://www.brenda-enzymes.org/enzyme.php?ecno=3.1.1.101 </ref>.
	It was in 2016, that Yoshida et al. discovered the bacterium Ideonella sakaiensis 201-F6 <ref name="discovery I. saka" />. The enzyme PETase allows this bacterium to grow by degrading PET (Polyethylene Terephthalate) that is used as its main carbon and energy source.		It was in 2016, that Yoshida et al. discovered the bacterium Ideonella sakaiensis 201-F6 <ref name="discovery I. saka" />. The enzyme PETase allows this bacterium to grow by degrading PET (Polyethylene Terephthalate) that is used as its main carbon and energy source.

Clara Felice at 22:28, 18 January 2022

Clara Felice — Tue, 18 Jan 2022 22:28:39 GMT

←Older revision		Revision as of 22:28, 18 January 2022
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	In mechanical recycling, collected and sorted PET waste can be powdered before melting and reprocessing to other forms. Chemical recycling degrades PET into its basic monomers which can then be polymerized again <ref name="current and futur perspectives" />. As biological recycling is cheaper, can be done with temperature conditions without the use of hazardous chemicals, by using microbial catalysis of polymer bond cleavage reactions and doesn’t use toxic reagents <ref name="current and futur perspectives" />, it is a sustainable alternative to mechanical recycling. However, bio-recycling is limited by the organism used, inherent polymer properties and the choice of pre-treatment, so modifications of these factors are to be explored before the PET hydrolase can be used in recycling processes.		In mechanical recycling, collected and sorted PET waste can be powdered before melting and reprocessing to other forms. Chemical recycling degrades PET into its basic monomers which can then be polymerized again <ref name="current and futur perspectives" />. As biological recycling is cheaper, can be done with temperature conditions without the use of hazardous chemicals, by using microbial catalysis of polymer bond cleavage reactions and doesn’t use toxic reagents <ref name="current and futur perspectives" />, it is a sustainable alternative to mechanical recycling. However, bio-recycling is limited by the organism used, inherent polymer properties and the choice of pre-treatment, so modifications of these factors are to be explored before the PET hydrolase can be used in recycling processes.

-	As a future challenge, we can think about the circular bioeconomy.	+	As a future challenge, we can think about the circular bioeconomy <ref name="current and futur perspectives" />.

	</StructureSection>		</StructureSection>
	== References ==		== References ==
	<references/>		<references/>