User:Braden Sciarra/Sandbox 1
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<StructureSection load='1F8I' size='340' side='right' caption='Isocitrate Lyase from ''Mycobacterium tuberculosis''' scene=''> | <StructureSection load='1F8I' size='340' side='right' caption='Isocitrate Lyase from ''Mycobacterium tuberculosis''' scene=''> | ||
[[Image:CAC.png|400 px|right|thumb|Figure 1: ICL mediated glyoxylate shunt pathway of the Citric Acid Cycle]] | [[Image:CAC.png|400 px|right|thumb|Figure 1: ICL mediated glyoxylate shunt pathway of the Citric Acid Cycle]] | ||
- | [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. 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>. | + | [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. 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="ICL"/>. |
== Structure == | == Structure == | ||
[[Image:homotetramer.png|150 px|left|thumb|Figure 2: C2 Symmetry of the homotetramer isocitrate lyase]] | [[Image:homotetramer.png|150 px|left|thumb|Figure 2: C2 Symmetry of the homotetramer isocitrate lyase]] | ||
- | The ICL homotetramer possesses C2 symmetry, with an axis of rotation at x-axis, y-axis, and z-axis of the enzyme. Two individual subunits off ICL 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 essentially be composed of two dimerized subunits. This interaction will bury approximately 18% of the surface of each subunit, and will help to shield the interior binding site from hydration. | + | The ICL homotetramer possesses C2 symmetry, with an axis of rotation at x-axis, y-axis, and z-axis of the enzyme. Two individual subunits off ICL 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 essentially be composed of two dimerized subunits<ref name="ICL">PMID2696959</ref>. 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 == | == Active Site == | ||
[[Image:Serine_with_active_site.png|400 px|right|thumb|Figure 3: Highly ordered hydrogen bonding network within the active site of ICL]] | [[Image:Serine_with_active_site.png|400 px|right|thumb|Figure 3: Highly ordered hydrogen bonding network within the active site of ICL]] | ||
- | The <scene name='69/697526/Binding_pocket/1'>Active Site</scene> of isocitrate lyase lies near the C-terminal ends of the Beta-strands of the active site. The glyoxylate substrate is held into place by a network 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 hydrogen bound 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>. | + | The <scene name='69/697526/Binding_pocket/1'>Active Site</scene> of isocitrate lyase lies near the C-terminal ends of the Beta-strands of the active site<ref name="ICL"/>. The glyoxylate substrate is held into place by a network 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 hydrogen bound 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=== | ===Catalytic Loop=== |
Revision as of 00:32, 8 April 2015
Isocitrate Lyase from Mycobacterium Tuberculosis
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References
- ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 Sharma V, Sharma S, Hoener zu Bentrup K, McKinney JD, Russell DG, Jacobs WR Jr, Sacchettini JC. Structure of isocitrate lyase, a persistence factor of Mycobacterium tuberculosis. Nat Struct Biol. 2000 Aug;7(8):663-8. PMID:10932251 doi:10.1038/77964
- ↑ 2.0 2.1 2.2 2.3 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