Sandbox Reserved 1844: Difference between revisions

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=Leaf Branch Compost Cutinase=

~~4EB0 [https://www.rcsb.org/structure/4EB0/ 4EBO] is the primary PDB file used throughout this page. The substrate added is 2-HE(MHET)₃, a trimer of MHET (mono-(2-hydroxy-ethyl) terephthalate).~~

==Introduction==

Leaf branch compost [https://en.wikipedia.org/wiki/Cutinase cutinase] <scene name='10/1075246/4eb0_in_pink/5'>(LCC)</scene> is a versatile enzyme that can break down both natural plant polymers and synthetic plastics.<ref name="Tournier">PMID:32269349</ref><ref name="Sui">PMID:37849919</ref> It was discovered in a [https://en.wikipedia.org/wiki/Compost compost] heap, and it originally evolved to degrade [https://en.wikipedia.org/wiki/Cutin cutin], the protective biopolymer in plant surfaces.<ref name="Ueda">PMID:34160605</ref><ref name="Kolattukudy">PMID:17779010</ref> LCC has also shown high efficiency in hydrolyzing [https://en.wikipedia.org/wiki/Polyethylene_terephthalate polyethylene terephthalate] (PET), which is a widely used plastic that contributes to pollution. Unlike many other PET-degrading enzymes, LCC is thermostable ''and'' has a high [https://en.wikipedia.org/wiki/Specificity_constant catalytic efficiency], which means it can function at temperatures that are optimal for industrial recycling processes.<ref name="Khairul">PMID:36293501</ref><ref name="Burgin">PMID:38538850</ref> By breaking PET into its monomers, LCC promotes [https://en.wikipedia.org/wiki/Closed-loop_recycling closed-loop recycling] of plastic waste and reduces environmental accumulation.<ref name="Sui"/>

[https://www.rcsb.org/structure/4EB0 4EB0] is the primary PDB file used throughout this page.<ref name=Sulaiman, S., You, D. J., Kanaya, E., Koga, Y. & Kanaya, S. Crystal structure and thermodynamic and kinetic stability of metagenome-derived LC-cutinase. Biochemistry 53, 1858–1869 (2014).> The protein is an LCC mutant that has been optimized for thermostability. The model substrate is 2-HE(MHET)₃, a trimer of MHET [https://en.wikipedia.org/wiki/2-Hydroxyethyl_terephthalic_acid (mono-(2-hydroxy-ethyl) terephthalate)]. MHET is an intermediate in the depolymerization of PET.<ref name="Zhang">PMID:37945666</ref><ref name="Tournier"/>

== Function ==

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== Structural Overview ==

LCC consists of one domain. <scene name='10/1075246/4eb0_helix_sheet/4'>Alpha helices and beta sheets</scene> are interspersed throughout the protein, with beta sheets (yellow) forming a stable central core surrounded by alpha helices (magenta) that contribute to the overall folding. This creates a predominantly α/β hydrolase fold that is typical of cutinases.

LCC consists of one domain. <scene name='10/1075246/4eb0_helix_sheet/5'>Alpha helices and beta sheets</scene> are interspersed throughout the protein, with beta sheets (yellow) forming a stable central core surrounded by alpha helices (magenta) that contribute to the overall folding. This creates a predominantly α/β hydrolase fold that is typical of cutinases.

=== Catalytic Triad ===

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=== Ligand Binding Pocket ===

The <scene name='10/1075246/4eb0_with_colored_ligand_stick/3'>substrate-binding site</scene> of LCC is a long, mainly hydrophobic groove that accommodates PET chains. This groove includes three subsites—designated −2, −1, and +~~1—that~~ interact with specific PET units near the scissile ester bond. Hydrophobic residues such as <scene name='10/1075248/4eb0_with_colored_ligand_stick/2'>F125, V212, M166, and F243</scene> line the groove and facilitate binding by interacting with the [https://en.wikipedia.org/wiki/Aromatic_compound aromatic] rings of the PET molecule. These interactions help align the substrate in the correct position for catalysis.

The <scene name='10/1075246/4eb0_with_colored_ligand_stick/3'>substrate-binding site</scene> of LCC is a long, mainly hydrophobic groove that accommodates PET chains. This groove includes three subsites—designated <scene name='10/1075246/4eb0_ligand_subsites/1'>−2, −1, and +1</scene>—that interact with specific PET units near the scissile ester bond. Hydrophobic residues such as <scene name='10/1075248/4eb0_with_colored_ligand_stick/2'>F125, V212, M166, and F243</scene> line the groove and facilitate binding by interacting with the [https://en.wikipedia.org/wiki/Aromatic_compound aromatic] rings of the PET molecule. These interactions help align the substrate in the correct position for catalysis.

The <scene name='10/1075248/4eb0_surface_w_stick_ligand/1'>molecular surface view of the enzyme-ligand interaction</scene> shows the overall shape and depth of the binding groove. The <scene name='10/1075246/4eb0_hydrophobicity_ligand/3'>cartoon representation of the enzyme-ligand interaction</scene>, the enzyme is shown as a ribbon diagram with the hydrophobic residues colored pink, to show how the PET chain fits snugly into the groove.

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 =Leaf Branch Compost Cutinase=
 <StructureSection load='4EB0_with_substrate.pdb' size='340' side='right' caption='Leaf Branch Compost Cutinase (PDB: 4EB0)' scene='10/1075246/4eb0_in_pink/5'>
-EB0 [https://www.rcsb.org/structure/4EB0/ 4EBO] is the primary PDB file used throughout this page. The substrate added is 2-HE(MHET)₃, a trimer of MHET (mono-(2-hydroxy-ethyl) terephthalate).
 ==Introduction==
 Leaf branch compost [https://en.wikipedia.org/wiki/Cutinase cutinase] <scene name='10/1075246/4eb0_in_pink/5'>(LCC)</scene> is a versatile enzyme that can break down both natural plant polymers and synthetic plastics.<ref name="Tournier">PMID:32269349</ref><ref name="Sui">PMID:37849919</ref> It was discovered in a [https://en.wikipedia.org/wiki/Compost compost] heap, and it originally evolved to degrade [https://en.wikipedia.org/wiki/Cutin cutin], the protective biopolymer in plant surfaces.<ref name="Ueda">PMID:34160605</ref><ref name="Kolattukudy">PMID:17779010</ref> LCC has also shown high efficiency in hydrolyzing [https://en.wikipedia.org/wiki/Polyethylene_terephthalate polyethylene terephthalate] (PET), which is a widely used plastic that contributes to pollution. Unlike many other PET-degrading enzymes, LCC is thermostable ''and'' has a high [https://en.wikipedia.org/wiki/Specificity_constant catalytic efficiency], which means it can function at temperatures that are optimal for industrial recycling processes.<ref name="Khairul">PMID:36293501</ref><ref name="Burgin">PMID:38538850</ref> By breaking PET into its monomers, LCC promotes [https://en.wikipedia.org/wiki/Closed-loop_recycling closed-loop recycling] of plastic waste and reduces environmental accumulation.<ref name="Sui"/>
+[https://www.rcsb.org/structure/4EB0 4EB0] is the primary PDB file used throughout this page.<ref name=Sulaiman, S., You, D. J., Kanaya, E., Koga, Y. & Kanaya, S. Crystal structure and thermodynamic and kinetic stability of metagenome-derived LC-cutinase. Biochemistry 53, 1858–1869 (2014).> The protein is an LCC mutant that has been optimized for thermostability. The model substrate is 2-HE(MHET)₃, a trimer of MHET [https://en.wikipedia.org/wiki/2-Hydroxyethyl_terephthalic_acid (mono-(2-hydroxy-ethyl) terephthalate)]. MHET is an intermediate in the depolymerization of PET.<ref name="Zhang">PMID:37945666</ref><ref name="Tournier"/>
 == Function ==
@@ Line 18: / Line 19: @@
 == Structural Overview ==
-LCC consists of one domain. <scene name='10/1075246/4eb0_helix_sheet/4'>Alpha helices and beta sheets</scene> are interspersed throughout the protein, with beta sheets (yellow) forming a stable central core surrounded by alpha helices (magenta) that contribute to the overall folding. This creates a predominantly α/β hydrolase fold that is typical of cutinases.
+LCC consists of one domain. <scene name='10/1075246/4eb0_helix_sheet/5'>Alpha helices and beta sheets</scene> are interspersed throughout the protein, with beta sheets (yellow) forming a stable central core surrounded by alpha helices (magenta) that contribute to the overall folding. This creates a predominantly α/β hydrolase fold that is typical of cutinases.
 === Catalytic Triad ===
@@ Line 26: / Line 27: @@
 === Ligand Binding Pocket ===
-The <scene name='10/1075246/4eb0_with_colored_ligand_stick/3'>substrate-binding site</scene> of LCC is a long, mainly hydrophobic groove that accommodates PET chains. This groove includes three subsites—designated −2, −1, and +1—that interact with specific PET units near the scissile ester bond. Hydrophobic residues such as <scene name='10/1075248/4eb0_with_colored_ligand_stick/2'>F125, V212, M166, and F243</scene> line the groove and facilitate binding by interacting with the [https://en.wikipedia.org/wiki/Aromatic_compound aromatic] rings of the PET molecule. These interactions help align the substrate in the correct position for catalysis.
+The <scene name='10/1075246/4eb0_with_colored_ligand_stick/3'>substrate-binding site</scene> of LCC is a long, mainly hydrophobic groove that accommodates PET chains. This groove includes three subsites—designated <scene name='10/1075246/4eb0_ligand_subsites/1'>−2, −1, and +1</scene>—that interact with specific PET units near the scissile ester bond. Hydrophobic residues such as <scene name='10/1075248/4eb0_with_colored_ligand_stick/2'>F125, V212, M166, and F243</scene> line the groove and facilitate binding by interacting with the [https://en.wikipedia.org/wiki/Aromatic_compound aromatic] rings of the PET molecule. These interactions help align the substrate in the correct position for catalysis.
 The <scene name='10/1075248/4eb0_surface_w_stick_ligand/1'>molecular surface view of the enzyme-ligand interaction</scene> shows the overall shape and depth of the binding groove. The <scene name='10/1075246/4eb0_hydrophobicity_ligand/3'>cartoon representation of the enzyme-ligand interaction</scene>, the enzyme is shown as a ribbon diagram with the hydrophobic residues colored pink, to show how the PET chain fits snugly into the groove.