Sandbox 201: Difference between revisions
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* <scene name='Sandbox_201/Atp_binding_site_grey/1'>ATP binding site</scene> | * <scene name='Sandbox_201/Atp_binding_site_grey/1'>ATP binding site</scene> | ||
:The N- and C-terminal domains are both able to form interactions with ATP and ATP analogues. But the ß-strands of the core region in the N-terminal domain contain most of the residues involved in binding ATP. <scene name='Sandbox_201/ | :The N- and C-terminal domains are both able to form interactions with ATP and ATP analogues. But the ß-strands of the core region in the N-terminal domain contain most of the residues involved in binding ATP. <scene name='Sandbox_201/Atp_binding_site_lys75/1'>Lys75</scene>, <scene name='Sandbox_201/Atp_binding_site_lys99/1'>Lys99</scene> (motif I), <scene name='Sandbox_201/Atp_binding_site_lys119/1'>Lys119</scene> (motif Ia), <scene name='Sandbox_201/Atp_binding_site_lys240/1'>Lys240</scene> (motif V), and <scene name='Sandbox_201/Atp_binding_site_lys242/1'>Lys242</scene> (motif V) interact with the phosphate groups of ATP and ATP analogues. | ||
:Lys99 is the site of adenylation in Rnl1, <ref>Thogersen, H. C., Morris, H. R., Rand, K. N., and Gait, M. J. (1985) Eur. J. Biochem. | :Lys99 is the site of adenylation in Rnl1, <ref>Thogersen, H. C., Morris, H. R., Rand, K. N., and Gait, M. J. (1985) Eur. J. Biochem. | ||
147, 325–329</ref> but in this structure this residue seems to be situated at a distance incompatible with covalent interaction with the phosphate of ATP (more than 3 Å).<ref name="main_article">K.El Omari, J.Ren, L.E.Bird, M.K.Bona, G.Klarmann, S.F.LeGrice, D.K.Stammers (2006) J. Biol. Chem. 281,1573-1579</ref> That could suggest that the formation of a covalent bond needs some conformational changes. But we do not know if a conformational change has to occur to allow the covalent bond formation, or if the formation of this bond leads to a conformational change. | 147, 325–329</ref> but in this structure this residue seems to be situated at a distance incompatible with covalent interaction with the phosphate of ATP (more than 3 Å).<ref name="main_article">K.El Omari, J.Ren, L.E.Bird, M.K.Bona, G.Klarmann, S.F.LeGrice, D.K.Stammers (2006) J. Biol. Chem. 281,1573-1579</ref> That could suggest that the formation of a covalent bond needs some conformational changes. But we do not know if a conformational change has to occur to allow the covalent bond formation, or if the formation of this bond leads to a conformational change. | ||
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* <scene name='Sandbox_201/Apc_binding_site/1'>AMPcPP binding site</scene> | * <scene name='Sandbox_201/Apc_binding_site/1'>AMPcPP binding site</scene> | ||
:T4 RNA ligase is also able to bind <scene name='Sandbox_201/Apc/1'>two AMPcPP</scene>. This molecule does not allow the nucleotidyltransferase function of the enzyme, but it seems necessary to Rnl1 cristallyzation. Each AMPcPP interacts via hydrogen bonds with ten residues (Tyr37, Arg54, Lys75, Tyr98, Lys99, Glu100, Lys119, Glu159, Lys 240 and Lys242), one Ca<sup>2+</sup>, one Mg<sup>2+</sup> and one Cl<sup>-</sup>. It also interacts with several other enzyme residues via hydrophobic interactions. | :T4 RNA ligase is also able to bind <scene name='Sandbox_201/Apc/1'>two AMPcPP</scene>. This molecule does not allow the nucleotidyltransferase function of the enzyme, but it seems necessary to Rnl1 cristallyzation. Each AMPcPP <scene name='Sandbox_201/Apc_ions_residues/2'>interacts via hydrogen bonds</scene> with ten residues (Tyr37, Arg54, Lys75, Tyr98, Lys99, Glu100, Lys119, Glu159, Lys 240 and Lys242), one Ca<sup>2+</sup>, one Mg<sup>2+</sup> and one Cl<sup>-</sup>. It also interacts with several other enzyme residues via hydrophobic interactions. | ||
</StructureSection> | </StructureSection> | ||
