User:Tsung-Yi Lin/Sandbox 1 - Revision history

Tsung-Yi Lin at 00:09, 21 April 2010

Tsung-Yi Lin — Wed, 21 Apr 2010 00:09:31 GMT

←Older revision		Revision as of 00:09, 21 April 2010
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	In nature, polyketides are synthesized by large multifunctional enzymes called polyketide synthases. Among several characterized PKSs, the biosynthesis of the polyketide Core of erythromycin A, 6-deoxyerythronolide B (6-dEB), has provided the paradigm for understanding the structure and function of the PKSs that are responsible for assembling complex polyketides .		In nature, polyketides are synthesized by large multifunctional enzymes called polyketide synthases. Among several characterized PKSs, the biosynthesis of the polyketide Core of erythromycin A, 6-deoxyerythronolide B (6-dEB), has provided the paradigm for understanding the structure and function of the PKSs that are responsible for assembling complex polyketides .

-	[[Image:DEBS.png\|frame\|6-deoxyerythronolide B synthase (DEBS)]]	+	[[Image:DEBS.png\|frame\|6-deoxyerythronolide B synthase (DEBS)\|left\|300px]]
	The 6-deoxyerythronolide B synthase (DEBS), which catalyzes the formation of 6-dEB, consists of three large polypeptides, DEBS1, DEBS2 and DEBS3, each 330 to 370 kD in size, and each polypeptide in DEBS is composed of two modules, where a module includes all the catalytic domains responsible for one round of chain extension and modification on the growing polyketide intermediate. Each module minimally contains three essential domains; a β-keto acyl synthase, simply referred to as ketosynthase (KS), an acyl transferase (AT) and an acyl carrier protein (ACP). All of them catalyze extender units adding to the growing polyketide chain. In detail, AT domain selects the appropriate monomer unit and transfers the carbon extender units from acyl-CoA metabolite onto the phosphopantetheinyl arm of ACP, and KS domains catalyzes decarboxylative condensation between the growing polyketide chain from the previous module and an ACP-bound extender unit.		The 6-deoxyerythronolide B synthase (DEBS), which catalyzes the formation of 6-dEB, consists of three large polypeptides, DEBS1, DEBS2 and DEBS3, each 330 to 370 kD in size, and each polypeptide in DEBS is composed of two modules, where a module includes all the catalytic domains responsible for one round of chain extension and modification on the growing polyketide intermediate. Each module minimally contains three essential domains; a β-keto acyl synthase, simply referred to as ketosynthase (KS), an acyl transferase (AT) and an acyl carrier protein (ACP). All of them catalyze extender units adding to the growing polyketide chain. In detail, AT domain selects the appropriate monomer unit and transfers the carbon extender units from acyl-CoA metabolite onto the phosphopantetheinyl arm of ACP, and KS domains catalyzes decarboxylative condensation between the growing polyketide chain from the previous module and an ACP-bound extender unit.

Tsung-Yi Lin at 00:08, 21 April 2010

Tsung-Yi Lin — Wed, 21 Apr 2010 00:08:04 GMT

←Older revision		Revision as of 00:08, 21 April 2010
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	A [[CBI Molecule]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].		A [[CBI Molecule]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

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	<applet load='2HG4' size='[450,338]' frame='true' align='right'		<applet load='2HG4' size='[450,338]' frame='true' align='right'
	caption='Structure of the ketosynthase-acyltransferase didomain of module 5 from DEBS. (2HG4)' scene='User:Tsung-Yi Lin/Sandbox_1/>		caption='Structure of the ketosynthase-acyltransferase didomain of module 5 from DEBS. (2HG4)' scene='User:Tsung-Yi Lin/Sandbox_1/>
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	<applet load='2JU1' size='[450,338]' frame='true' align='right'		<applet load='2JU1' size='[450,338]' frame='true' align='right'
-	caption='Solution structure of acyl carrier protein domain from module 2 of 6-deoxyerythronolide B synthase (DEBS) (2JU1)'scene='User:Tsung-Yi Lin/Sandbox_1/>	+	caption='Solution structure of acyl carrier protein domain from module 2 of 6-deoxyerythronolide B synthase (DEBS) (2JU1)' scene='User:Tsung-Yi Lin/Sandbox_1/>

Tsung-Yi Lin at 00:04, 21 April 2010

Tsung-Yi Lin — Wed, 21 Apr 2010 00:04:16 GMT

←Older revision		Revision as of 00:04, 21 April 2010
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	A [[CBI Molecule]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].		A [[CBI Molecule]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].
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	Polyketides are a large class of natural products produced by bacteria, fungi, and plants. Polyketides exhibit diverse structures and a wide variety of biological activities, which includes antibiotic, antitumor, anticancer, and other biological properties.		Polyketides are a large class of natural products produced by bacteria, fungi, and plants. Polyketides exhibit diverse structures and a wide variety of biological activities, which includes antibiotic, antitumor, anticancer, and other biological properties.

-	In nature, polyketides are synthesized by large multifunctional enzymes called polyketide synthases. Among several characterized PKSs, the biosynthesis of the polyketide Core of erythromycin A, 6-deoxyerythronolide B (6-dEB~~) (Fig. 2~~), has provided the paradigm for understanding the structure and function of the PKSs that are responsible for assembling complex polyketides .	+	In nature, polyketides are synthesized by large multifunctional enzymes called polyketide synthases. Among several characterized PKSs, the biosynthesis of the polyketide Core of erythromycin A, 6-deoxyerythronolide B (6-dEB), has provided the paradigm for understanding the structure and function of the PKSs that are responsible for assembling complex polyketides .

	[[Image:DEBS.png\|frame\|6-deoxyerythronolide B synthase (DEBS)]]		[[Image:DEBS.png\|frame\|6-deoxyerythronolide B synthase (DEBS)]]

Tsung-Yi Lin at 00:02, 21 April 2010

Tsung-Yi Lin — Wed, 21 Apr 2010 00:02:58 GMT

←Older revision		Revision as of 00:02, 21 April 2010
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-	~~[[Image:DEBS.png\|frame\|6-deoxyerythronolide B synthase (DEBS)]]~~	+

	A [[CBI Molecule]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].		A [[CBI Molecule]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].
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	In nature, polyketides are synthesized by large multifunctional enzymes called polyketide synthases. Among several characterized PKSs, the biosynthesis of the polyketide Core of erythromycin A, 6-deoxyerythronolide B (6-dEB) (Fig. 2), has provided the paradigm for understanding the structure and function of the PKSs that are responsible for assembling complex polyketides .		In nature, polyketides are synthesized by large multifunctional enzymes called polyketide synthases. Among several characterized PKSs, the biosynthesis of the polyketide Core of erythromycin A, 6-deoxyerythronolide B (6-dEB) (Fig. 2), has provided the paradigm for understanding the structure and function of the PKSs that are responsible for assembling complex polyketides .

-		+	[[Image:DEBS.png\|frame\|6-deoxyerythronolide B synthase (DEBS)]]
	The 6-deoxyerythronolide B synthase (DEBS), which catalyzes the formation of 6-dEB, consists of three large polypeptides, DEBS1, DEBS2 and DEBS3, each 330 to 370 kD in size, and each polypeptide in DEBS is composed of two modules, where a module includes all the catalytic domains responsible for one round of chain extension and modification on the growing polyketide intermediate. Each module minimally contains three essential domains; a β-keto acyl synthase, simply referred to as ketosynthase (KS), an acyl transferase (AT) and an acyl carrier protein (ACP). All of them catalyze extender units adding to the growing polyketide chain. In detail, AT domain selects the appropriate monomer unit and transfers the carbon extender units from acyl-CoA metabolite onto the phosphopantetheinyl arm of ACP, and KS domains catalyzes decarboxylative condensation between the growing polyketide chain from the previous module and an ACP-bound extender unit.		The 6-deoxyerythronolide B synthase (DEBS), which catalyzes the formation of 6-dEB, consists of three large polypeptides, DEBS1, DEBS2 and DEBS3, each 330 to 370 kD in size, and each polypeptide in DEBS is composed of two modules, where a module includes all the catalytic domains responsible for one round of chain extension and modification on the growing polyketide intermediate. Each module minimally contains three essential domains; a β-keto acyl synthase, simply referred to as ketosynthase (KS), an acyl transferase (AT) and an acyl carrier protein (ACP). All of them catalyze extender units adding to the growing polyketide chain. In detail, AT domain selects the appropriate monomer unit and transfers the carbon extender units from acyl-CoA metabolite onto the phosphopantetheinyl arm of ACP, and KS domains catalyzes decarboxylative condensation between the growing polyketide chain from the previous module and an ACP-bound extender unit.

Tsung-Yi Lin at 00:02, 21 April 2010

Tsung-Yi Lin — Wed, 21 Apr 2010 00:02:24 GMT

←Older revision		Revision as of 00:02, 21 April 2010
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-	[[Image:~~intactModelLargeText~~.~~jpg~~\|frame\|~~Bacterial chemotaxis receptor~~]]	+	[[Image:DEBS.png\|frame\|6-deoxyerythronolide B synthase (DEBS)]]

	A [[CBI Molecule]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].		A [[CBI Molecule]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

Tsung-Yi Lin at 23:55, 20 April 2010

Tsung-Yi Lin — Tue, 20 Apr 2010 23:55:11 GMT

←Older revision		Revision as of 23:55, 20 April 2010
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	A [[CBI Molecule]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].		A [[CBI Molecule]] being studied in the [http://www.umass.edu/cbi/ University of Massachusetts Amherst Chemistry-Biology Interface Program] at UMass Amherst and on display at the [http://www.molecularplayground.org/ Molecular Playground].

-	~~Many~~ bacteria ~~can "smell" their surroundings~~ and ~~"choose" where to go~~. ~~They detect molecules such as amino acids or sugars using receptors that bind these molecules~~ and ~~transmit~~ a ~~signal into the cell~~. ~~This signal controls~~ several ~~proteins which ultimately control~~ the ~~direction of rotation~~ of the ~~motors that rotate the flagella~~. ~~One direction causes the cell to continue swimming; the other direction causes the cell to tumble. When an attractant molecule binds~~, the ~~receptor signals: "Things look good, keep swimming!" The opposite signal occurs when bacteria sense a repellant or less attractant molecules: "Time to tumble~~ and ~~try a new swimming direction~~."	+
		+	Polyketides are a large class of natural products produced by bacteria, fungi, and plants. Polyketides exhibit diverse structures and a wide variety of biological activities, which includes antibiotic, antitumor, anticancer, and other biological properties.
		+
		+	In nature, polyketides are synthesized by large multifunctional enzymes called polyketide synthases. Among several characterized PKSs, the biosynthesis of the polyketide Core of erythromycin A, 6-deoxyerythronolide B (6-dEB) (Fig. 2), has provided the paradigm for understanding the structure and function of the PKSs that are responsible for assembling complex polyketides .


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	<applet load='2HG4' size='[450,338]' frame='true' align='right'		<applet load='2HG4' size='[450,338]' frame='true' align='right'
	caption='Structure of the ketosynthase-acyltransferase didomain of module 5 from DEBS. (2HG4)' scene='User:Tsung-Yi Lin/Sandbox_1/>		caption='Structure of the ketosynthase-acyltransferase didomain of module 5 from DEBS. (2HG4)' scene='User:Tsung-Yi Lin/Sandbox_1/>
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	<applet load='2JU1' size='[450,338]' frame='true' align='right'		<applet load='2JU1' size='[450,338]' frame='true' align='right'
	caption='Solution structure of acyl carrier protein domain from module 2 of 6-deoxyerythronolide B synthase (DEBS) (2JU1)'scene='User:Tsung-Yi Lin/Sandbox_1/>		caption='Solution structure of acyl carrier protein domain from module 2 of 6-deoxyerythronolide B synthase (DEBS) (2JU1)'scene='User:Tsung-Yi Lin/Sandbox_1/>
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	<applet load='3EL6' size='[450,338]' frame='true' align='right'		<applet load='3EL6' size='[450,338]' frame='true' align='right'
	caption='Crystal Structure of the Erythromycin Dehydratase (3EL6)' scene='User:Tsung-Yi Lin/Sandbox_1/>		caption='Crystal Structure of the Erythromycin Dehydratase (3EL6)' scene='User:Tsung-Yi Lin/Sandbox_1/>
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Tsung-Yi Lin at 23:52, 20 April 2010

Tsung-Yi Lin — Tue, 20 Apr 2010 23:52:13 GMT

←Older revision		Revision as of 23:52, 20 April 2010
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-	~~A bacterial chemotaxis receptor is an unusually long alpha-helical structure.~~ The ~~attractant molecule~~ (~~the ligand~~) ~~binds near~~ the ~~top~~ of ~~this picture~~ and ~~sends~~ a ~~signal across~~ the ~~membrane into the cell to control proteins that bind near~~ the ~~bottom~~. ~~This is~~ a ~~model~~ of the ~~structure of~~ the ~~receptor based on experimental structures~~ of ~~pieces of related proteins~~.	+	The 6-deoxyerythronolide B synthase (DEBS), which catalyzes the formation of 6-dEB, consists of three large polypeptides, DEBS1, DEBS2 and DEBS3, each 330 to 370 kD in size, and each polypeptide in DEBS is composed of two modules, where a module includes all the catalytic domains responsible for one round of chain extension and modification on the growing polyketide intermediate. Each module minimally contains three essential domains; a β-keto acyl synthase, simply referred to as ketosynthase (KS), an acyl transferase (AT) and an acyl carrier protein (ACP). All of them catalyze extender units adding to the growing polyketide chain. In detail, AT domain selects the appropriate monomer unit and transfers the carbon extender units from acyl-CoA metabolite onto the phosphopantetheinyl arm of ACP, and KS domains catalyzes decarboxylative condensation between the growing polyketide chain from the previous module and an ACP-bound extender unit.
-		+
-		+

		+	After the extender unit was added onto the elongating polyketide chain, it can be further processed by optional tailoring domains, including ketoreductases (KRs), dehydratases (DHs), and enoyl reductases (ERs), to change the oxidation state of each ketide-unit and to yield a hydroxyl, enoyl, or methylene group that may be present in the final product. In addition, the thioesterase (TE) domain that located at the C-terminus of module 6 of DEBS catalyzes the macrocyclization and releases the final product 6-dEB.


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	<applet load='2HG4' size='[450,338]' frame='true' align='right'		<applet load='2HG4' size='[450,338]' frame='true' align='right'
	caption='Structure of the ketosynthase-acyltransferase didomain of module 5 from DEBS. (2HG4)' scene='User:Tsung-Yi Lin/Sandbox_1/>		caption='Structure of the ketosynthase-acyltransferase didomain of module 5 from DEBS. (2HG4)' scene='User:Tsung-Yi Lin/Sandbox_1/>
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	<applet load='2JU1' size='[450,338]' frame='true' align='right'		<applet load='2JU1' size='[450,338]' frame='true' align='right'
	caption='Solution structure of acyl carrier protein domain from module 2 of 6-deoxyerythronolide B synthase (DEBS) (2JU1)'scene='User:Tsung-Yi Lin/Sandbox_1/>		caption='Solution structure of acyl carrier protein domain from module 2 of 6-deoxyerythronolide B synthase (DEBS) (2JU1)'scene='User:Tsung-Yi Lin/Sandbox_1/>
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	<applet load='3EL6' size='[450,338]' frame='true' align='right'		<applet load='3EL6' size='[450,338]' frame='true' align='right'
	caption='Crystal Structure of the Erythromycin Dehydratase (3EL6)' scene='User:Tsung-Yi Lin/Sandbox_1/>		caption='Crystal Structure of the Erythromycin Dehydratase (3EL6)' scene='User:Tsung-Yi Lin/Sandbox_1/>
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Tsung-Yi Lin at 03:27, 17 April 2010

Tsung-Yi Lin — Sat, 17 Apr 2010 03:27:48 GMT

←Older revision		Revision as of 03:27, 17 April 2010
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	A bacterial chemotaxis receptor is an unusually long alpha-helical structure. The attractant molecule (the ligand) binds near the top of this picture and sends a signal across the membrane into the cell to control proteins that bind near the bottom. This is a model of the structure of the receptor based on experimental structures of pieces of related proteins.		A bacterial chemotaxis receptor is an unusually long alpha-helical structure. The attractant molecule (the ligand) binds near the top of this picture and sends a signal across the membrane into the cell to control proteins that bind near the bottom. This is a model of the structure of the receptor based on experimental structures of pieces of related proteins.

-	===DH===

-	<applet load='~~3EL6~~' size='[450,338]' frame='true' align='right'	+
-	caption='~~Crystal~~ Structure of the ~~Erythromycin Dehydratase~~ (~~3EL6~~)' scene='User:Tsung-Yi Lin/Sandbox_1/>	+
		+
		+	===KS-AT===
		+
		+	<applet load='2HG4' size='[450,338]' frame='true' align='right'
		+	caption='Structure of the ketosynthase-acyltransferase didomain of module 5 from DEBS. (2HG4)' scene='User:Tsung-Yi Lin/Sandbox_1/>
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-	===KS-AT===

-	<applet load='~~2HG4~~' size='[450,338]' frame='true' align='right'	+
-	caption='Structure of the ~~ketosynthase-acyltransferase didomain of module 5 from DEBS.~~ (~~2HG4~~)' scene='User:Tsung-Yi Lin/Sandbox_1/>	+
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		+	===DH===
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		+	<applet load='3EL6' size='[450,338]' frame='true' align='right'
		+	caption='Crystal Structure of the Erythromycin Dehydratase (3EL6)' scene='User:Tsung-Yi Lin/Sandbox_1/>
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Tsung-Yi Lin at 03:26, 17 April 2010

Tsung-Yi Lin — Sat, 17 Apr 2010 03:26:49 GMT

←Older revision		Revision as of 03:26, 17 April 2010
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	<applet load='3EL6' size='[450,338]' frame='true' align='right'		<applet load='3EL6' size='[450,338]' frame='true' align='right'
-	caption='Crystal Structure of the Erythromycin Dehydratase (3EL6)' scene='User:Tsung-Yi Lin/Sandbox_1~~/Loadedfrompdb/1'~~/>	+	caption='Crystal Structure of the Erythromycin Dehydratase (3EL6)' scene='User:Tsung-Yi Lin/Sandbox_1/>
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	<applet load='2JU1' size='[450,338]' frame='true' align='right'		<applet load='2JU1' size='[450,338]' frame='true' align='right'
-	caption='Solution structure of acyl carrier protein domain from module 2 of 6-deoxyerythronolide B synthase (DEBS) (2JU1)'scene='User:Tsung-Yi Lin/Sandbox_1~~/Loadedfrompdb/1'~~/>	+	caption='Solution structure of acyl carrier protein domain from module 2 of 6-deoxyerythronolide B synthase (DEBS) (2JU1)'scene='User:Tsung-Yi Lin/Sandbox_1/>
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	<applet load='2HG4' size='[450,338]' frame='true' align='right'		<applet load='2HG4' size='[450,338]' frame='true' align='right'
	caption='Structure of the ketosynthase-acyltransferase didomain of module 5 from DEBS. (2HG4)' scene='User:Tsung-Yi Lin/Sandbox_1/>		caption='Structure of the ketosynthase-acyltransferase didomain of module 5 from DEBS. (2HG4)' scene='User:Tsung-Yi Lin/Sandbox_1/>
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	===TE===		===TE===

	<applet load='1MO2' size='[450,338]' frame='true' align='right'		<applet load='1MO2' size='[450,338]' frame='true' align='right'
-	caption='Thioesterase Domain from 6-Deoxyerythronolide Synthase (DEBS TE)(1MO2)' scene='User:Tsung-Yi Lin/Sandbox_1~~/Loadedfrompdb/1'~~/>	+	caption='Thioesterase Domain from 6-Deoxyerythronolide Synthase (DEBS TE)(1MO2)' scene='User:Tsung-Yi Lin/Sandbox_1/>

Tsung-Yi Lin: /* KS-AT */

Tsung-Yi Lin — Sat, 17 Apr 2010 03:25:42 GMT

KS-AT

←Older revision		Revision as of 03:25, 17 April 2010
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	<applet load='2HG4' size='[450,338]' frame='true' align='right'		<applet load='2HG4' size='[450,338]' frame='true' align='right'
-	caption='Structure of the ketosynthase-acyltransferase didomain of module 5 from DEBS. (2HG4)' scene='User:Tsung-Yi Lin/Sandbox_1~~/Loadedfrompdb/1'~~/>	+	caption='Structure of the ketosynthase-acyltransferase didomain of module 5 from DEBS. (2HG4)' scene='User:Tsung-Yi Lin/Sandbox_1/>
-		+
-		+
-		+

	===TE===		===TE===