Sandbox Reserved 660: Difference between revisions
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[[Image:The image of interaction.png | thumb]] | [[Image:The image of interaction.png | thumb]] | ||
The AMP <scene name='Sandbox_Reserved_660/Act_site/1'>binding pocket</scene> is mainly located within the N-domain. The highly conserved sequence which corresponds to <scene name='Sandbox_Reserved_660/Binding_site/1'>Q328GYGMTEA335</scene> in 4CL provides the majority of the surface of the binding pocket. The side chain phenyl group of Tyr-330 provide the Van Der Waals interaction to the adenine group of the bound AMP on one side of the | The AMP <scene name='Sandbox_Reserved_660/Act_site/1'>binding pocket</scene> is mainly located within the N-domain. The highly conserved sequence which corresponds to <scene name='Sandbox_Reserved_660/Binding_site/1'>Q328GYGMTEA335</scene> in 4CL provides the majority of the surface of the binding pocket. The side chain phenyl group of Tyr-330 provide the Van Der Waals interaction to the adenine group of the bound AMP on one side of the adenine ring and on the other side, the adenine group is support by the side chain of Gly-306 and main chain of Ala-307. The N atoms of adenine group could also donate hydrogen bond to the carbonyl oxygen of Gly-329. Several hydrogen bonds are formed between the ribose oxygen atoms and the side chains of Arg-432, Lys-434, and Lys-438 and the phosphate group could also form hydrogen bond with side chain of Thr-333 and Gln-443 and main chain NH of Thr-333[3]. | ||
The <scene name='Sandbox_Reserved_660/Cata_site/1'>Catalytic site</scene> of the 4CL is located on Lys-523 on the C domain and Lys-438 and Gln-443 on the N domain. there is a Ligand Binding–Induced Conformational Changes, and the conformational changes, was observed in 4CL1 structures upon the binding of AMP. A large cleft was observed between the N- and C-domains in apo-4CL1 (unmodified) and the cleft is closed by an 81˚ rotation of the C-domain relative to the N-domain upon the AMP binding. Because no major internal changes are found in either the N- or C-domain, the closure of the inter domain cleft upon the binding of AMP is a rigid-body movement[4]. The Inter domain movement brings different catalytic residues from the C-domains to substrate binding sites to catalyze the respective partial reactions, such as the adenylate-forming partial reaction, and the thioester-forming partial reaction. | The <scene name='Sandbox_Reserved_660/Cata_site/1'>Catalytic site</scene> of the 4CL is located on Lys-523 on the C domain and Lys-438 and Gln-443 on the N domain. there is a Ligand Binding–Induced Conformational Changes, and the conformational changes, was observed in 4CL1 structures upon the binding of AMP. A large cleft was observed between the N- and C-domains in apo-4CL1 (unmodified) and the cleft is closed by an 81˚ rotation of the C-domain relative to the N-domain upon the AMP binding. Because no major internal changes are found in either the N- or C-domain, the closure of the inter domain cleft upon the binding of AMP is a rigid-body movement[4]. The Inter domain movement brings different catalytic residues from the C-domains to substrate binding sites to catalyze the respective partial reactions, such as the adenylate-forming partial reaction, and the thioester-forming partial reaction. | ||
