Sandbox Reserved 1056: Difference between revisions
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== 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. Tan molecules represent amino acid side chains. Yellow molecules represent substrates. The magnesium cation is represented by the large, green sphere.]] | [[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 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> | <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=== | ===Catalytic Loop=== | ||