Sandbox 201: Difference between revisions

Line 48:

* <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/~~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.

: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/Lys75_green_ball_v1/1'>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.

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.

Sandbox 201: Difference between revisions

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@@ Line 48: / Line 48: @@
 * <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/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.
+: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/Lys75_green_ball_v1/1'>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.
 , 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.