Sandbox Reserved 1056 - Revision history

Douglas Schnell at 13:49, 14 March 2017

Douglas Schnell — Tue, 14 Mar 2017 13:49:48 GMT

←Older revision		Revision as of 13:49, 14 March 2017
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	== Structural highlights ==		== Structural highlights ==
	[[Image:Hydrophobic_C-terminal_Side_Chain_Binding_Site_with_Y248.png\|200 px\|left\|thumb\|Carboxypeptidase A in ''B. taurus.'' The red highlights the hydrophobic binding pocket while the blue highlights Y248.]]		[[Image:Hydrophobic_C-terminal_Side_Chain_Binding_Site_with_Y248.png\|200 px\|left\|thumb\|Carboxypeptidase A in ''B. taurus.'' The red highlights the hydrophobic binding pocket while the blue highlights Y248.]]
-	To the left is the ~~<scene name='69/694223/Hydrophobic_binding_pocket/1'>~~hydrophobic binding pocket~~</scene>~~ of Carboxypeptidase A in ''B. taurus,'' one of the ~~molecules~~ most important structural features. This binding pocket is the site at which C-terminal side chain of the substrate binds. It is formed by amino acid residues I243, I247, A250, G252, G253, S254 and I255.	+	Shown to the left is the hydrophobic binding pocket of Carboxypeptidase A in ''B. taurus'' in relation to the whole molecule. It is one of the molecule's most important structural features. The <scene name='69/694223/Hydrophobic_binding_pocket_2/2'>hydrophobic binding pocket</scene> is also isolated in the 3D applet to the right. This binding pocket is the site at which C-terminal side chain of the substrate binds. It is formed by amino acid residues I243, I247, A250, G252, G253, S254 and I255.

	Nearby, there is also Y198 which serves as the recognition site for the sidechain next to the C-terminal residue.		Nearby, there is also Y198 which serves as the recognition site for the sidechain next to the C-terminal residue.

Douglas Schnell at 13:43, 14 March 2017

Douglas Schnell — Tue, 14 Mar 2017 13:43:25 GMT

←Older revision		Revision as of 13:43, 14 March 2017
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	{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->		{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
	==Carboxypeptidase A in ''B. taurus''==		==Carboxypeptidase A in ''B. taurus''==
-	<StructureSection load='~~1stp~~' size='340' side='right' caption='Caption for this structure' scene=''>	+	<StructureSection load='1cpx' size='340' side='right' caption='Caption for this structure' scene=''>
-	~~This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.~~	+
	You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.		You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

	===Introduction===		===Introduction===
-	===Instructions===
-	Click above on '''edit this page''' to modify. Be careful with the < and > signs.
-	You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

	== Biological Function ==		== Biological Function ==

Douglas Schnell at 13:26, 14 March 2017

Douglas Schnell — Tue, 14 Mar 2017 13:26:23 GMT

←Older revision		Revision as of 13:26, 14 March 2017
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	== Structural highlights ==		== Structural highlights ==
	[[Image:Hydrophobic_C-terminal_Side_Chain_Binding_Site_with_Y248.png\|200 px\|left\|thumb\|Carboxypeptidase A in ''B. taurus.'' The red highlights the hydrophobic binding pocket while the blue highlights Y248.]]		[[Image:Hydrophobic_C-terminal_Side_Chain_Binding_Site_with_Y248.png\|200 px\|left\|thumb\|Carboxypeptidase A in ''B. taurus.'' The red highlights the hydrophobic binding pocket while the blue highlights Y248.]]
-	To the left is the hydrophobic binding pocket of Carboxypeptidase A in ''B. taurus,'' one of the molecules most important structural features. This binding pocket is the site at which C-terminal side chain of the substrate binds. It is formed by amino acid residues I243, I247, A250, G252, G253, S254 and I255.	+	To the left is the <scene name='69/694223/Hydrophobic_binding_pocket/1'>hydrophobic binding pocket</scene> of Carboxypeptidase A in ''B. taurus,'' one of the molecules most important structural features. This binding pocket is the site at which C-terminal side chain of the substrate binds. It is formed by amino acid residues I243, I247, A250, G252, G253, S254 and I255.

	Nearby, there is also Y198 which serves as the recognition site for the sidechain next to the C-terminal residue.		Nearby, there is also Y198 which serves as the recognition site for the sidechain next to the C-terminal residue.
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	== References ==		== References ==
	<references/>		<references/>
-
-	Bukrinsky, J.T., Bjerrum, M.J. and Kadziola, A. (1998), Native Carboxypeptidase A in a New Crystal Environment Reveals a Different Conformation of the Important Tyrosine 248. Biochem., 37:16555-16564.

Douglas Schnell at 13:14, 14 March 2017

Douglas Schnell — Tue, 14 Mar 2017 13:14:01 GMT

←Older revision		Revision as of 13:14, 14 March 2017
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	== Structural Overview ==		== Structural Overview ==
-	[[Image:Hydrophobic_C-terminal_Side_Chain_Binding_Site_with_Y248.png\|100 px\|left\|thumb\|Figure Legend]]

	== Structural highlights ==		== Structural highlights ==
-	To the left is the ~~<scene name='75/752345/Hydrophobic_binding_pocket/1'>~~hydrophobic binding pocket~~</scene>~~ of Carboxypeptidase A in ''B. ~~Taurus~~,'' one of the molecules most important structural features. This binding pocket is the site at which C-terminal side chain of the substrate binds. It is formed by amino acid residues I243, I247, A250, G252, G253, S254 and I255.	+	[[Image:Hydrophobic_C-terminal_Side_Chain_Binding_Site_with_Y248.png\|200 px\|left\|thumb\|Carboxypeptidase A in ''B. taurus.'' The red highlights the hydrophobic binding pocket while the blue highlights Y248.]]
-	~~<Structure load='1CPX' size='350' frame='true' align='right' caption='This is a 3D image of Carboxypeptidase A in ''B. Taurus.'' ' scene='' />~~	+	To the left is the hydrophobic binding pocket of Carboxypeptidase A in ''B. taurus,'' one of the molecules most important structural features. This binding pocket is the site at which C-terminal side chain of the substrate binds. It is formed by amino acid residues I243, I247, A250, G252, G253, S254 and I255.
		+
	Nearby, there is also Y198 which serves as the recognition site for the sidechain next to the C-terminal residue.		Nearby, there is also Y198 which serves as the recognition site for the sidechain next to the C-terminal residue.

Douglas Schnell at 13:07, 14 March 2017

Douglas Schnell — Tue, 14 Mar 2017 13:07:43 GMT

←Older revision		Revision as of 13:07, 14 March 2017
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	== Structural highlights ==		== Structural highlights ==
		+	To the left is the <scene name='75/752345/Hydrophobic_binding_pocket/1'>hydrophobic binding pocket</scene> of Carboxypeptidase A in ''B. Taurus,'' one of the molecules most important structural features. This binding pocket is the site at which C-terminal side chain of the substrate binds. It is formed by amino acid residues I243, I247, A250, G252, G253, S254 and I255.
	<Structure load='1CPX' size='350' frame='true' align='right' caption='This is a 3D image of Carboxypeptidase A in ''B. Taurus.'' ' scene='' />		<Structure load='1CPX' size='350' frame='true' align='right' caption='This is a 3D image of Carboxypeptidase A in ''B. Taurus.'' ' scene='' />
-		+	Nearby, there is also Y198 which serves as the recognition site for the sidechain next to the C-terminal residue.
-	~~This~~ is the ~~<scene name='75/752345/Hydrophobic_binding_pocket/1'>hydrophobic binding pocket</scene> of Carboxypeptidase A in ''B. Taurus~~.''	+

	== Mechanism of Action ==		== Mechanism of Action ==

Douglas Schnell at 12:53, 14 March 2017

Douglas Schnell — Tue, 14 Mar 2017 12:53:58 GMT

←Older revision		Revision as of 12:53, 14 March 2017
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	== Structural highlights ==		== Structural highlights ==
-	<Structure load='1CPX' size='350' frame='true' align='right' caption='This is a 3D image of Carboxypeptidase A in ''B. Taurus.'' ' scene='~~(Hydrophobic binding pocket)~~' />	+	<Structure load='1CPX' size='350' frame='true' align='right' caption='This is a 3D image of Carboxypeptidase A in ''B. Taurus.'' ' scene='' />

	This is the <scene name='75/752345/Hydrophobic_binding_pocket/1'>hydrophobic binding pocket</scene> of Carboxypeptidase A in ''B. Taurus.''		This is the <scene name='75/752345/Hydrophobic_binding_pocket/1'>hydrophobic binding pocket</scene> of Carboxypeptidase A in ''B. Taurus.''

Douglas Schnell at 12:48, 14 March 2017

Douglas Schnell — Tue, 14 Mar 2017 12:48:34 GMT

←Older revision		Revision as of 12:48, 14 March 2017
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	== References ==		== References ==
	<references/>		<references/>
		+
	Bukrinsky, J.T., Bjerrum, M.J. and Kadziola, A. (1998), Native Carboxypeptidase A in a New Crystal Environment Reveals a Different Conformation of the Important Tyrosine 248. Biochem., 37:16555-16564.		Bukrinsky, J.T., Bjerrum, M.J. and Kadziola, A. (1998), Native Carboxypeptidase A in a New Crystal Environment Reveals a Different Conformation of the Important Tyrosine 248. Biochem., 37:16555-16564.

Douglas Schnell at 12:46, 14 March 2017

Douglas Schnell — Tue, 14 Mar 2017 12:46:31 GMT

←Older revision		Revision as of 12:46, 14 March 2017
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	== References ==		== References ==
	<references/>		<references/>
		+	Bukrinsky, J.T., Bjerrum, M.J. and Kadziola, A. (1998), Native Carboxypeptidase A in a New Crystal Environment Reveals a Different Conformation of the Important Tyrosine 248. Biochem., 37:16555-16564.

Douglas Schnell at 03:18, 13 March 2017

Douglas Schnell — Mon, 13 Mar 2017 03:18:58 GMT

←Older revision		Revision as of 03:18, 13 March 2017
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	{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->		{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
-	==~~Your Protein Name here~~==	+	==Carboxypeptidase A in ''B. taurus''==
	<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>		<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
	This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.		This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
		+	You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.
		+
		+	===Introduction===
		+	===Instructions===
		+	Click above on '''edit this page''' to modify. Be careful with the < and > signs.
	You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.		You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

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	== Structural Overview ==		== Structural Overview ==
		+	[[Image:Hydrophobic_C-terminal_Side_Chain_Binding_Site_with_Y248.png\|100 px\|left\|thumb\|Figure Legend]]
		+
		+	== Structural highlights ==
		+	<Structure load='1CPX' size='350' frame='true' align='right' caption='This is a 3D image of Carboxypeptidase A in ''B. Taurus.'' ' scene='(Hydrophobic binding pocket)' />
		+
		+	This is the <scene name='75/752345/Hydrophobic_binding_pocket/1'>hydrophobic binding pocket</scene> of Carboxypeptidase A in ''B. Taurus.''

	== Mechanism of Action ==		== Mechanism of Action ==

Geoffrey C. Hoops at 20:42, 26 February 2017

Geoffrey C. Hoops — Sun, 26 Feb 2017 20:42:43 GMT

←Older revision		Revision as of 20:42, 26 February 2017
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-	==~~Isocitrate Lyase from ''Mycobacterium Tuberculosis''~~==	+	{{Sandbox_Reserved_Butler_CH462_Sp2015_#}}<!-- PLEASE ADD YOUR CONTENT BELOW HERE -->
-	<StructureSection load='~~1F8I~~' size='340' side='right' caption='~~Isocitrate Lyase from~~ ''~~Mycobacterium tuberculosis~~''' ~~scene=~~'~~Isocitrate Lyase complex~~ with ~~glyoxylate~~ and ~~succinate ligands bound'~~>	+	==Your Protein Name here==
		+	<StructureSection load='1stp' size='340' side='right' caption='Caption for this structure' scene=''>
		+	This is a default text for your page ''''''. Click above on '''edit this page''' to modify. Be careful with the < and > signs.
		+	You may include any references to papers as in: the use of JSmol in Proteopedia <ref>DOI 10.1002/ijch.201300024</ref> or to the article describing Jmol <ref>PMID:21638687</ref> to the rescue.

-	[[Image:Glyox_Shunt.png\|400 px\|right\|thumb\|Figure 1: ICL mediated glyoxylate shunt pathway of the Citric Acid Cycle. The intermediates of the CAC are shown in blue, while the glyoxylate shunt pathway intermediates are shown in green.]]	+	== Biological Function ==
-	[http://en.wikipedia.org/wiki/Isocitrate_lyase Isocitrate Lyase] (ICL) is a metabolic enzyme that converts the metabolite isocitrate into glyoxylate and succinate. ICL is a homotetramer with each monomer being composed of 14 alpha helices, 14 beta sheets, and a magnesium ion cofactor. ICL has shown clinical relevance in the disease state [http://en.wikipedia.org/wiki/Tuberculosis Tuberculosis] where it is responsible for the persistence of ''Mycobacterium tuberculosis'' during the chronic stage of infection.<ref name="genes">PMID: 18054522</ref> This survival strategy mediated by ICL is characterized by a metabolic shortcut within the [http://en.wikipedia.org/wiki/Citric_acid_cycle Citric Acid Cycle]. ICL creates this shunt pathway by converting isocitrate to succinate and glyoxylate, diverting acetyl-CoA from the beta-oxidation of fatty acids.<ref name=~~"ICL">PMID:10932251</ref><ref name~~=~~"ICL2">PMID: 2696959</ref>~~	+

-	== ~~Structure~~ ==	+	== Structural Overview ==
-	~~[[Image:homotetramer.png\|150 px\|left\|thumb\|Figure 2: 222 Symmetry of the homotetramer isocitrate lyase. Each identical monomer is shown in a unique color.]]~~	+
-	The ICL homotetramer possesses 222 symmetry, with an axis of rotation about the x-axis, y-axis, and z-axis of the enzyme. Two individual subunits of ICL, shown here as blue and green, are held together by a characteristic <scene name='69/697526/Helix_swapping/3'>Helix Swapping</scene> between three alpha helices formed by residues 370-384, 349-367, and 399-409 on neighboring monomers.<ref name="ICL">PMID:10932251</ref> The interlocking mechanism created by these helices provides additional strength to hold the two monomeric subunits together, allowing ICL to be composed of a dimer of dimers.<ref name="ICL2"/> This interaction will bury approximately 18% of the surface of each subunit, and will help to shield the interior binding site from hydration.	+

-	== ~~Active Site ==~~	+	== Mechanism of Action ==
-	~~[[Image:Serine_with_active_site.png\|400 px\|right\|thumb\|Figure 3: Highly ordered hydrogen bonding network within the active site~~ of ~~ICL. Tan molecules represent amino acid side chains. Yellow molecules represent substrates. The magnesium cation is represented by the large, green sphere.]]~~	+
-	~~The active site of isocitrate lyase lies near the C-terminal ends of the Beta-strands of the active site.<ref name~~=~~"ICL2"/> The <scene name~~='69/697526/Binding_pocket/1'>Active Site</scene> is shown here with ligands bound (purple) and catalytic residues shown (gray) in coordination with the magnesium ion (green). The glyoxylate substrate is held into place by a <scene name='69/694223/Serine_and_gly_bond/2'>Network</scene> of hydrogen bonds with Ser 91, Gly 92, Trp 93, and Arg 228.<ref name="ICL">PMID:10932251</ref> The magnesium ion serves to stabilize the partial negative charge placed on the carbonyl oxygens of the glyoxylate. The other substrate, succinate, contains two carboxyl groups and possesses a similar network of hydrogen bonding that holds the ligand in place within the active site. One carboxylate group is hydrogen bound to Asn 313, Glu 295, Arg 228, and Gly 192. The second carboxylate is	+
-	<scene name='69/694223/Second_carboxylate/5'>Hydrogen Bound</scene> to Thr 347, Asn 313, Ser 315, Ser 317, and His 193.<ref name="ICL">PMID:10932251</ref> The ordered hydrogen bonding within the active site orients the succinate molecule such that the alpha carbon is only 3.2 angstroms away from the deprotonated thiol group of Cys 191.<ref name="ICL">PMID:10932251</ref><ref name="claisen">Masamune et al. Bio-Claisen condensation catalyzed by thiolase from Zoogloea ramigera. Active site cysteine residues. "Journal of the American Chemical Society" 111: 1879-1881 (1989). DOI: 10.1021/ja00187a053</ref>	+

-	==~~=Catalytic Loop===~~	+	== Zinc Ligand(s) ==
-	[[Image:Openvsclosed..png\|400 px\|left\|thumb\|Figure 4: Open (Blue) vs. Closed (Red) conformation of the active site loop of ICL. Glyoxylate is shown in yellow and succinate in purple. Hydrogen bonding is shown between LYS189 and the catalytic loop.]]	+
-	The catalytic loop of the Isocitrate Lyase enzyme is composed of residues 185-196, and can exist in both the open and closed conformation (see Figure 4). In the open conformation, the catalytic loop is oriented such that the catalytic CYS191 residue is located far from the active site, allowing for solvent accessibility and substrate binding.<ref name="solvent">Connely, M. L. Solvent-accessible surfaces of proteins and nucleic acids "Science" 221:709-713 (~~1983~~)~~. DOI: 10.1126/science.6879170</ref> Upon substrate binding, the catalytic loop, shown in blue, adopts a <scene name~~=~~'69/694223/Catalytic_loop/2'>closed loop</scene> conformation, moving between ten and fifteen angstroms.<ref name~~="ICL">PMID:10932251</ref> This closed conformation will cause the binding site to become inaccessible to the solvent. The loop closure is triggered by the movement of the Mg ion that occurs upon binding of the succinate. This movement of the Mg ion results in electrostatic interactions at LYS189, causing the loop to close.	+

-	==~~Elucidation of ICL Structure Using Inhibitors~~==	+	== Other Ligands ==
-	~~[[Image:Inhibitors57.png\|400 px\|right\|thumb\|Figure 5: Substrate inhibitors of Isocitrate Lyase used to elucidate the first crystal structure of ICL.]]~~	+
-	The two inhibitors used to elucidate the structure of ICL were 3-nitropropionate and 3-bromopyruvate. The 3-nitropropionate was used to mimic the succinate, while the 3-bromopyruvate is used to mimic the glyoxylate. These two inhibitors have also been shown to be good inhibitors of isocitrate lyase in ''M. avium'' indicating that their inhibitory capacity is conserved across multiple species.<ref name="ICL">PMID:10932251</ref> A mutant isocitrate lyase C191S, in conjunction with the aforementioned substrate mimics, was used to elucidate the first high resolution crystal structure of ICL.<ref name="ICL">PMID:10932251</ref> Dehalogenated 3-bromopyruvate works to inhibit isocitrate lyase by forming a covalent bond with the Ser191 in the active site, which can be found crystallized here [[1f8m]]. This 3-bromopyruvate occupies the same site that the succinate would occupy. The C191S mutant adopts a conformation almost identical to the CYS191 residue in the wild type indicating that this is an accurate depiction of the conformation. <ref name="ICL">PMID:10932251</ref>	+

-	~~==Mechanism==~~	+	This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.
-	~~[[Image:Real_Mechanism.png\|400 px\|right\|thumb\|Figure 6: Chemical Mechanism of Isocitrate Lyase. Note: The mechanism depicted in this image~~ is ~~the reverse process, but the mechanism is identical.]]~~	+
-	~~Isocitrate lyase catalyzes~~ a ~~reversible aldol condensation, converting isocitrate~~ to ~~glyoxylate and succinate via the breaking of a C-C bond.~~<~~ref~~ name=~~"claisen~~"/~~> Within the active site of ICL the HIS193 residue deprotonates the <scene name='69~~/~~694223~~/~~Arginine~~/3'>~~Cys191~~</scene> ~~residue of the active site in order~~ to ~~increase its basicity.~~<~~ref~~ name="~~ICL">PMID:10932251<~~/~~ref><ref name=~~"~~claisen"/~~> ~~The Cys 191 residue then deprotonates the alpha carbon adjacent to one of the carbonyl groups of succinate, thus forming the enolic intermediate.~~<~~ref name="claisen"~~/> ~~The negatively charged alpha carbon atom~~ of the ~~enolic intermediate acts as a nucleophile that attacks the carbonyl carbon of the aldehyde of glyoxylate~~. ~~The nucleophilic attack will place a negative charge~~ on ~~the oxygen atom oxygen at the former carbonyl oxygen of the aldehyde, which will be stabilized by positive charges of the Mg ion, ARG228~~ and ~~HIS180.<ref name="ICL">PMID:10932251</ref> The protonation~~ of ~~this species will yield the final product. It is important to note that this reaction is entirely reversible; the breakdown of isocitrate into glyoxylate and succinate occurs using a similar mechanism~~.	+
-		+

	</StructureSection>		</StructureSection>
-	==3D Structures of Isocitrate Lyase==
-
-	Updated on {{REVISIONDAY2}}-{{MONTHNAME\|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
-
-	*From ''Mycobacterium Tuberculosis''
-	**[[1f61]] ICL apoenzyme <br />
-	**[[1f8m]] 3-bromopyruvate modified ICL <br />
-
-	*ICL from other bacteria
-	**[[3i4e]] ICL from ''B. pesudomallei''
-	**[[3p0x]], [[3eol]], [[3oq8]], [[3e5b]] ICL from ''B. melitensis''
-	**[[3lg3]] ICL from ''Y. pestis'' CO92
-	**[[1dqu]] ICL from ''A. nidulans''
-	**[[1igw]] ICL from the A216C mutant of ''E. coli''
-
	== References ==		== References ==
	<references/>		<references/>