Difference between revisions of "Team: Purdue/Enzymes"

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<h2> Project Description </h2>
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<h1> Enzymes </h1>
  
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<p>Tell us about your project, describe what moves you and why this is something important for your team.</p>
 
 
<br />
 
<br />
 +
<h2>Lignin Peroxidase</h2>
 +
<p>Is an enzyme that is the initiator and one of the main enzymes responsible for the breakdown of lignin inside the cell walls of plant cells. Reticulitermes flavipes, or the eastern subterranean termite, uses this enzyme to digest woody debris with higher efficiency. Lignin peroxidase has the ability to oxidize aromatic compounds in lignin with redox potentials above 1.4 eV, which is the equivalent to reducing metals like gold or molecules such as lead oxide. It is believed that this action is done by catalyzing the transfer of an oxygen atom from a hydrogen peroxide molecule to an aromatic ring. However, the exact redox mechanism for lignin peroxidase is currently unknown.</p>
  
−
<h5>What should this page contain?</h5>
+
<div>1,2-bis(3,4-dimethoxyphenyl)propane-1,3-diol + H2O2 → 3,4-dimethoxybenzaldehyde +
 +
1-(3,4-dimethoxyphenyl)ethane-1,2-diol + H2O</div>
 +
<img src="https://static.igem.org/mediawiki/2015/0/04/Purdue_Lignan_Peroxidase.jpeg" alt="Enzymatic activity of Lignan Peroxidase" style="width:433px;height:280px;">
 +
<div>pH Range</div>
 +
<div>6.8-7.2</div>
 +
<div>Temperature Range</div>
 +
<div> 30-37 degrees C</div>
 +
 
 +
<br />
 +
<h2>Versatile Peroxidase</h2>
 +
<p>Is a hemoprotein (iron-requiring) enzyme that was selected for inclusion in our project due to its adaptability - it has active sites identical to both lignin peroxidase and manganese peroxidase, aiding the efficiency of wood digestion in the fungus Colletotrichum fioriniae. Versatile peroxidase catalyzes the reaction of a substrate and peroxidase into an oxidized product and water.</p>
 +
<img src="https://static.igem.org/mediawiki/2015/a/ad/Purdue_Versatile_Peroxidase.png" alt="Enzymatic diagram of Versatile Peroxidase" style="width:223px;height:199px;">
 +
<div>An illustration of VP. (Versatile Peroxidase Involved in the Natural Degradation of Lignin)</div>
 
<ul>
 
<ul>
−
<li> A clear and concise description of your project.</li>
+
<li>pH Range: 5-6.8</li>
−
<li>A detailed explanation of why your team chose to work on this particular project.</li>
+
 
−
<li>References and sources to document your research.</li>
+
<li>Temperature Range: 25-28 degrees C</li>
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<li>Use illustrations and other visual resources to explain your project.</li>
+
 
</ul>
 
</ul>
  
  
 
<br />
 
<br />
−
<h4>Advice on writing your Project Description</h4>
+
<h2>Manganese Peroxidase</h2>
 +
<p>Is an enzyme that is capable of oxidizing of Mn^2+ ions into Mn^3+ ions by using an irreversible redox reaction with the aid of fungal chelators such as oxalic acid . This enzyme is specifically used by Heterobasidion irregulare TC 32-1, a variety of white rot fungus, to break down any wooden material in it’s path. Although the enzyme itself is not directly linked to lignin breakdown, the Mn^3+ ions that it creates are then able to attack and oxidize organic molecules such as phenolic substrates or several lignin compounds. These lignin compounds are broken down into free radicals which quickly degrade due to their molecular instability. Note: Calcium ions and heme-B are involved with the enzyme’s mechanism.</p>
 +
<div>2 Mn(II) + 2 H+ + H2O2 → 2 Mn(III) + 2 H2O</div>
 +
<img src="https://static.igem.org/mediawiki/2015/8/8e/Purdue_Maganese_Peroxidase.jpeg" alt="Enzymatic activity of Manganese Peroxidase" style="width:584px;height:311px;">
 +
<h4>Sources:</h4>
  
−
<p>
+
<ul>
−
We encourage you to put up a lot of information and content on your wiki, but we also encourage you to include summaries as much as possible. If you think of the sections in your project description as the sections in a publication, you should try to be consist, accurate and unambiguous in your achievements.  
+
<li>Piontek, K., Smith, A., & Blodig, W. (2001, May 29). Lignin peroxidase structure and function. Retrieved September 16, 2015, from http://www.ncbi.nlm.nih.gov/pubmed/11356137 </li>
−
</p>
+
  
−
<p>
+
<li>Sigma-Aldrich (accessed 2015, September 17). Lignin Peroxidase. http://www.sigmaaldrich.com/catalog/product/sigma/42603?lang=en&region=US</li>
−
Judges like to read your wiki and know exactly what you have achieved. This is how you should think about these sections; from the point of view of the judge evaluating you at the end of the year.
+
 
−
</p>
+
<li>Basic Format: Acalgaro. (2013).  Mangenese Peroxidase Mechanism [PNG]. Retrieved from https://commons.wikimedia.org/wiki/File:Manganese_peroxidase_mechanism.png</li>
 +
 
 +
<li>Hofrichter, M. (2002). Review: Lignin conversion by manganese peroxidase (MnP). Retrieved September 16, 2015, from http://www.sciencedirect.com/science/article/pii/S0141022901005282</li>
 +
 
 +
<li>Manganese peroxidase (CAS 114995-15-2). (2007). Retrieved September 16, 2015, from http://www.scbt.com/datasheet-211772-manganese-peroxidase.html </li>
 +
 
 +
</ul>
  
  
 
<br />
 
<br />
−
<h4>References</h4>
+
<h2>Laccase</h2>
−
<p>iGEM teams are encouraged to record references you use during the course of your research. They should be posted somewhere on your wiki so that judges and other visitors can see how you though about your project and what works inspired you.</p>
+
<p>Laccase is a copper-containing enzyme obtained from the gut rumen of Reticulitermes flavipes (the eastern subterranean termite), where its evolutionary uniqueness in its ability to efficiently degrade the lignin of woody debris when working in concert with other lignocellulases. Laccase functions via the catalyzation of one-electron substrate oxidations with a concurrent four-electron reduction of molecular oxygen to water. Unlike the peroxidases, they only require oxygen for activity, and are not dependant on peroxide.</p>
 +
<img src="https://static.igem.org/mediawiki/2015/b/b7/Purdue_Laccase.jpeg" alt="Diagram of Laccase enzymatic activity" style="width:523px;height:410px;">
 +
<div>Laccase as an enzyme during the degradation of lignin (Recent Advances)</div>
  
 +
<ul>
 +
<li>pH Range</li>
 +
<li>7-7.5</li>
  
 +
<li>Temperature Range</li>
 +
<li>20-25 degrees C</li>
 +
</ul>
 +
<h4>Sources:</h4>
 +
<ul>
 +
<li>MR Coy, TZ Salem, and JS Denton, et al. "Phenol-oxidizing Laccases from the Termite Gut." Science Direct. Insect Biochemistry and Molecular Biology, 1 Oct. 2010. Web. 18 Sept. 2015.</li>
  
−
<h4>Inspiration</h4>
+
<li>Cohen, R., L. Persky, and Y. Hadar. "Biotechnological Applications and Potential of Wood-degrading Mushrooms of the Genus Pleurotus." National Center for Biotechnology Information. U.S. National Library of Medicine, 15 Feb. 2002. Web. 18 Sept. 2015.</li>
−
<p>See how other teams have described and presented their projects: </p>
+
 
 +
<li>RECENT ADVANCES OF LACCASE ENZYME IN INDUSTRIAL BIOTECHNOLOGY : A REVIEW." PharmaTutor. Web. 19 Sept. 2015.</li>
 +
 
 +
<li>Scharf, Michael, and Aurélien Tartar. "Termite Digestomes as Sources for Novel Lignocellulases." Wiley Online Library. Biofuels, Bioproducts and Biorefining, 1 Nov. 2008. Web. 19 Sept. 2015.</li>
 +
</ul>
 +
<br />
 +
<h2>Tyrosinase</h2>
 +
<p>Is an oxidase that was included in our organism design not for its ability to digest lignin, but its function is the rate-limiting enzyme in the production of melanin. Obtained from Aspergillus fumigatus, Tyrosinase carries out the oxidation of phenols such as tyrosine and dopamine using dioxygen (O2). In the presence of catechol, benzoquinone is formed and the hydrogens removed from catechol combine with oxygen to form water.</p>
 +
<img src="https://static.igem.org/mediawiki/2015/2/23/Purdue_Tyrosinase_diagram.png" alt="Diagram of Tyrosinase enzymatic activity" style="width:510px;height:311px;">
 +
<p>Tyrosinase oxidizing the reaction of tyrosine and dopamine to produce dehydrated catechol and formation of benzoquinone (Tyrosinase reaction)</p>
  
 
<ul>
 
<ul>
−
<li><a href="https://2014.igem.org/Team:Imperial/Project"> Imperial</a></li>
+
<li>pH range</li>
−
<li><a href="https://2014.igem.org/Team:UC_Davis/Project_Overview"> UC Davis</a></li>
+
<li>6-7</li>
−
<li><a href="https://2014.igem.org/Team:SYSU-Software/Overview">SYSU Software</a></li>
+
 
 +
<li>Optimum Temperature</li>
 +
<li>30 degrees C</li>
 
</ul>
 
</ul>
  
 +
<br>
 +
<h4>References</h4>
 +
<ul>
 +
<li>Hearing, VJ, TM Ekel, PM Montague, and JM Nicholson. "Mammalin Tyrosinase. Stoichiometry and Measurement of Reaction Products." National Center for Biotechnology Information. U.S. National Library of Medicine, 18 Feb. 1980. Web. 18 Sept. 2015.</li>
 +
 +
<li>Photo:  "Tyrosinase reaction." Wikipedia. Wikipedia, 2 Mar. 2008. Web. 18 Sept. 2015.</li>
 +
<li>https://commons.wikimedia.org/wiki/File:Tyrosinase_reaction.PNG</li>
 +
</ul>
 +
 +
 +
<br />
 +
<h4>Aldo-Keto Reductase</h4>
 +
<h4>Aldo-Keto Reductase</h4>
 +
<p>Aldo-Keto Reductases are a family of enzymes with NADPH dependent oxidoreductases. Oxidoreductases work in the transfer of electrons, moving electrons from one molecule to another, or from reductants to oxidants. AKRs are expressed in all plants and animals. They play a role in the human body working to detoxify pharmaceuticals and drugs in the liver. Aldo-keto reductases (AKRs) have also been found to be highly expressed in the termite gut. A similar mechanism occurs in the termite gut, where toxins released from the breakdown of lignin are mediated by AKRs. AKRs have a beta-alpha-beta fold which binds via a NADP-binding motif. According to Dr. Michael Scharf, these aldo-keto reductases work as helper enzymes that exponentially aid in the digestion and breakdown of lignin, but are not as effective on their own.</p>
 +
<br>
 +
<div>pH Range (including optimal):  4.5-9.5 Optimal: 7 </div>
 +
<div>Temperature Range (including optimal): 0-55 C Optimal: 25-37</div>
 +
<br>
 +
<h4>Sources:</h4>
 +
<div>The aldo-keto reductase superfamily and its role in drug metabolism and detoxification. (n.d.). NCBI. Retrieved September 10, 2015, from http://www.ncbi.nlm.nih.gov/pubmed/18949601 </a></div>
 +
<br>
 +
<h4>Cellulase</h4>
 +
<p>Cellulase is an enzyme that plays a large role in the decomposition of cellulose. Specifically this enzyme works on the hydrolysis of the beta glycosidic linkages, precisely 1,4-beta-D-glycosidic linkages, in cellulose. Cellulase is not present in the human body, therefore the cellulose present in plant materials that are consumed never become broken down and are passed through the body. The main function of cellulase is to break down cellulose into monosaccharides or oligosaccharides that can be used in several ways. Cellulase is often used to make the raw materials in plants soluble for use in products like juices, alcoholic beverages, feed additives, and washing agents. </p>
 +
<img src="https://static.igem.org/mediawiki/2015/f/fa/BackgroundCelluloseChemicalStructure.jpg" alt="Cellulose Structure" style="width:457px;height:321px;">
 +
<br>
 +
<h4>Sources:</h4>
 +
<div>Cellulase. (n.d.). Worthington Biochemical Corporation. Retrieved September 17, 2015, from http://www.worthington-biochem.com/cel/default.html </a></div>
 +
 +
<div> Cellulase. GMO Compass Database (n.d.). Retrieved September 17, 2015, from http://www.worthington-biochem.com/cel/default.html </a></div>
 +
 +
<div>Cell wall components.(Image.) Retrieved September 9, 2015. http://www.intechopen.com/source/html/45622/media/image1.jpeg </a></div>
 +
 +
<br />
 +
<h4>Xylanase</h4>
 +
<p>Xylanase is an enzyme responsible for breaking down xylan, a sticky substance that like cellulose, is a component of the cell wall in plants that is not easily broken down. Xylans are made of five and six carbon ring polysaccharides. Xylan is dispersed evenly throughout the cell wall, connecting cellulose components. This is achieved by degrading beta-1,4- xylan into a simple sugar, xylose. Xylanases are used primarily in baking and alcoholic beverages, but also in producing starch for the textile industry. </p>
 +
<img src="https://static.igem.org/mediawiki/2015/d/d4/BackgroundXylanaseDiagramPlantCellWall.jpeg" alt="Cell Wall Diagram" style="width:228px;height:337px;">
 +
<br>
 +
<h4>Sources:</h4>
 +
<div> Scharf, Michael. (n.d.). Lignin-associated metagene expression in a lignocellulose-digesting termite. Retrieved August 24, 2015, from http://www.researchgate.net/publication/232738047_Lignin-associated_metagene_expression_in_a_lignocellulose-digesting_termite </a></div>
 +
 +
<div> Xylanase. GMO Compass Database (n.d.). Retrieved August 24, 2015 from http://www.gmo-compass.org/eng/database/enzymes/96.xylanase.html </a></div>
 
</div>
 
</div>
 
</html>
 
</html>

Latest revision as of 01:41, 20 November 2015

Team Banner

Enzymes


Lignin Peroxidase

Is an enzyme that is the initiator and one of the main enzymes responsible for the breakdown of lignin inside the cell walls of plant cells. Reticulitermes flavipes, or the eastern subterranean termite, uses this enzyme to digest woody debris with higher efficiency. Lignin peroxidase has the ability to oxidize aromatic compounds in lignin with redox potentials above 1.4 eV, which is the equivalent to reducing metals like gold or molecules such as lead oxide. It is believed that this action is done by catalyzing the transfer of an oxygen atom from a hydrogen peroxide molecule to an aromatic ring. However, the exact redox mechanism for lignin peroxidase is currently unknown.

1,2-bis(3,4-dimethoxyphenyl)propane-1,3-diol + H2O2 → 3,4-dimethoxybenzaldehyde + 1-(3,4-dimethoxyphenyl)ethane-1,2-diol + H2O
Enzymatic activity of Lignan Peroxidase
pH Range
6.8-7.2
Temperature Range
30-37 degrees C

Versatile Peroxidase

Is a hemoprotein (iron-requiring) enzyme that was selected for inclusion in our project due to its adaptability - it has active sites identical to both lignin peroxidase and manganese peroxidase, aiding the efficiency of wood digestion in the fungus Colletotrichum fioriniae. Versatile peroxidase catalyzes the reaction of a substrate and peroxidase into an oxidized product and water.

Enzymatic diagram of Versatile Peroxidase
An illustration of VP. (Versatile Peroxidase Involved in the Natural Degradation of Lignin)
  • pH Range: 5-6.8
  • Temperature Range: 25-28 degrees C

Manganese Peroxidase

Is an enzyme that is capable of oxidizing of Mn^2+ ions into Mn^3+ ions by using an irreversible redox reaction with the aid of fungal chelators such as oxalic acid . This enzyme is specifically used by Heterobasidion irregulare TC 32-1, a variety of white rot fungus, to break down any wooden material in it’s path. Although the enzyme itself is not directly linked to lignin breakdown, the Mn^3+ ions that it creates are then able to attack and oxidize organic molecules such as phenolic substrates or several lignin compounds. These lignin compounds are broken down into free radicals which quickly degrade due to their molecular instability. Note: Calcium ions and heme-B are involved with the enzyme’s mechanism.

2 Mn(II) + 2 H+ + H2O2 → 2 Mn(III) + 2 H2O
Enzymatic activity of Manganese Peroxidase

Sources:

  • Piontek, K., Smith, A., & Blodig, W. (2001, May 29). Lignin peroxidase structure and function. Retrieved September 16, 2015, from http://www.ncbi.nlm.nih.gov/pubmed/11356137
  • Sigma-Aldrich (accessed 2015, September 17). Lignin Peroxidase. http://www.sigmaaldrich.com/catalog/product/sigma/42603?lang=en&region=US
  • Basic Format: Acalgaro. (2013). Mangenese Peroxidase Mechanism [PNG]. Retrieved from https://commons.wikimedia.org/wiki/File:Manganese_peroxidase_mechanism.png
  • Hofrichter, M. (2002). Review: Lignin conversion by manganese peroxidase (MnP). Retrieved September 16, 2015, from http://www.sciencedirect.com/science/article/pii/S0141022901005282
  • Manganese peroxidase (CAS 114995-15-2). (2007). Retrieved September 16, 2015, from http://www.scbt.com/datasheet-211772-manganese-peroxidase.html

Laccase

Laccase is a copper-containing enzyme obtained from the gut rumen of Reticulitermes flavipes (the eastern subterranean termite), where its evolutionary uniqueness in its ability to efficiently degrade the lignin of woody debris when working in concert with other lignocellulases. Laccase functions via the catalyzation of one-electron substrate oxidations with a concurrent four-electron reduction of molecular oxygen to water. Unlike the peroxidases, they only require oxygen for activity, and are not dependant on peroxide.

Diagram of Laccase enzymatic activity
Laccase as an enzyme during the degradation of lignin (Recent Advances)
  • pH Range
  • 7-7.5
  • Temperature Range
  • 20-25 degrees C

Sources:

  • MR Coy, TZ Salem, and JS Denton, et al. "Phenol-oxidizing Laccases from the Termite Gut." Science Direct. Insect Biochemistry and Molecular Biology, 1 Oct. 2010. Web. 18 Sept. 2015.
  • Cohen, R., L. Persky, and Y. Hadar. "Biotechnological Applications and Potential of Wood-degrading Mushrooms of the Genus Pleurotus." National Center for Biotechnology Information. U.S. National Library of Medicine, 15 Feb. 2002. Web. 18 Sept. 2015.
  • RECENT ADVANCES OF LACCASE ENZYME IN INDUSTRIAL BIOTECHNOLOGY : A REVIEW." PharmaTutor. Web. 19 Sept. 2015.
  • Scharf, Michael, and Aurélien Tartar. "Termite Digestomes as Sources for Novel Lignocellulases." Wiley Online Library. Biofuels, Bioproducts and Biorefining, 1 Nov. 2008. Web. 19 Sept. 2015.

Tyrosinase

Is an oxidase that was included in our organism design not for its ability to digest lignin, but its function is the rate-limiting enzyme in the production of melanin. Obtained from Aspergillus fumigatus, Tyrosinase carries out the oxidation of phenols such as tyrosine and dopamine using dioxygen (O2). In the presence of catechol, benzoquinone is formed and the hydrogens removed from catechol combine with oxygen to form water.

Diagram of Tyrosinase enzymatic activity

Tyrosinase oxidizing the reaction of tyrosine and dopamine to produce dehydrated catechol and formation of benzoquinone (Tyrosinase reaction)

  • pH range
  • 6-7
  • Optimum Temperature
  • 30 degrees C

References

  • Hearing, VJ, TM Ekel, PM Montague, and JM Nicholson. "Mammalin Tyrosinase. Stoichiometry and Measurement of Reaction Products." National Center for Biotechnology Information. U.S. National Library of Medicine, 18 Feb. 1980. Web. 18 Sept. 2015.
  • Photo: "Tyrosinase reaction." Wikipedia. Wikipedia, 2 Mar. 2008. Web. 18 Sept. 2015.
  • https://commons.wikimedia.org/wiki/File:Tyrosinase_reaction.PNG

Aldo-Keto Reductase

Aldo-Keto Reductase

Aldo-Keto Reductases are a family of enzymes with NADPH dependent oxidoreductases. Oxidoreductases work in the transfer of electrons, moving electrons from one molecule to another, or from reductants to oxidants. AKRs are expressed in all plants and animals. They play a role in the human body working to detoxify pharmaceuticals and drugs in the liver. Aldo-keto reductases (AKRs) have also been found to be highly expressed in the termite gut. A similar mechanism occurs in the termite gut, where toxins released from the breakdown of lignin are mediated by AKRs. AKRs have a beta-alpha-beta fold which binds via a NADP-binding motif. According to Dr. Michael Scharf, these aldo-keto reductases work as helper enzymes that exponentially aid in the digestion and breakdown of lignin, but are not as effective on their own.


pH Range (including optimal): 4.5-9.5 Optimal: 7
Temperature Range (including optimal): 0-55 C Optimal: 25-37

Sources:

The aldo-keto reductase superfamily and its role in drug metabolism and detoxification. (n.d.). NCBI. Retrieved September 10, 2015, from http://www.ncbi.nlm.nih.gov/pubmed/18949601

Cellulase

Cellulase is an enzyme that plays a large role in the decomposition of cellulose. Specifically this enzyme works on the hydrolysis of the beta glycosidic linkages, precisely 1,4-beta-D-glycosidic linkages, in cellulose. Cellulase is not present in the human body, therefore the cellulose present in plant materials that are consumed never become broken down and are passed through the body. The main function of cellulase is to break down cellulose into monosaccharides or oligosaccharides that can be used in several ways. Cellulase is often used to make the raw materials in plants soluble for use in products like juices, alcoholic beverages, feed additives, and washing agents.

Cellulose Structure

Sources:

Cellulase. (n.d.). Worthington Biochemical Corporation. Retrieved September 17, 2015, from http://www.worthington-biochem.com/cel/default.html
Cellulase. GMO Compass Database (n.d.). Retrieved September 17, 2015, from http://www.worthington-biochem.com/cel/default.html
Cell wall components.(Image.) Retrieved September 9, 2015. http://www.intechopen.com/source/html/45622/media/image1.jpeg

Xylanase

Xylanase is an enzyme responsible for breaking down xylan, a sticky substance that like cellulose, is a component of the cell wall in plants that is not easily broken down. Xylans are made of five and six carbon ring polysaccharides. Xylan is dispersed evenly throughout the cell wall, connecting cellulose components. This is achieved by degrading beta-1,4- xylan into a simple sugar, xylose. Xylanases are used primarily in baking and alcoholic beverages, but also in producing starch for the textile industry.

Cell Wall Diagram

Sources:

Scharf, Michael. (n.d.). Lignin-associated metagene expression in a lignocellulose-digesting termite. Retrieved August 24, 2015, from http://www.researchgate.net/publication/232738047_Lignin-associated_metagene_expression_in_a_lignocellulose-digesting_termite
Xylanase. GMO Compass Database (n.d.). Retrieved August 24, 2015 from http://www.gmo-compass.org/eng/database/enzymes/96.xylanase.html