Sandbox 208: Difference between revisions

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*'''GDI-Rab Binding Platform (RBP)''', with β strands e1 and e3 and helix C, which form a separate binding site. This platform is located in domain I and interacts with the globular part of the Rab molecule. The RabGDI binding epitope contains a great number of conserved residues on Rab: Ile41, Gly42, Asp/Glu44 and Phe45 from Switch I; Trp62, Asp63, Ala65, Gln67, Phe/Tyr70, Thr/Ala72, Thr74, Ser/Thr75, Ser/Ala76 and Arg79 from Switch II. More precisely, the RBP is an essential structural element which form a great number of interactions with the C-terminus and Switch I of Rab. Three additional invariable residues are located on RBP, and form hydrogen bonds with the switch I region and the C-terminus of Rab.

*'''GDI C-terminus Coordinating Region (CCR) or C-terminus Binding Region (CBR)'''. The CBR represents a hydrophobic cavity on the GDI surface. In fact, this region is located in the cleft between domain I and domain II. It is formed by <scene name='Sandbox_208/Residues_93-112_domain_i/1'>residues 93-112</scene> from domain I and <scene name='Sandbox_208/Residues_226-235_domain_ii/1'>residues 226-235</scene> from domain II. The CBR coordinates the flexible extended C-terminus of Rab. In most cases, the CBR is occupied by side chains of hydrophobic residues of the Rab C-terminus tail. Hydrophobic contacts between GDI and Rab are supported by a hydrogen bond involving main chain atoms. Rab primary structure analysis revealed the presence of a Rab C-terminus characteristic sequence (AXA box), with two conserved aliphatic amino acid residues (Val191 and Leu193). Mutations of one of these residues induce a decrease of Rab affinity to GDI. Therefore, the AXA box contributes to increase Rab binding affinity to GDI upon complex formation.

*'''GDI C-terminus Coordinating Region (CCR) or C-terminus Binding Region (CBR)'''. The CBR represents a hydrophobic cavity on the GDI surface. In fact, this region is located in the cleft between domain I and domain II. It is formed by <scene name='Sandbox_208/Residues_93-112_domain_i/2'>residues 93-112</scene> from domain I and <scene name='Sandbox_208/Residues_226-235_domain_ii/2'>residues 226-235</scene> from domain II. The CBR coordinates the flexible extended C-terminus of Rab. In most cases, the CBR is occupied by side chains of hydrophobic residues of the Rab C-terminus tail. Hydrophobic contacts between GDI and Rab are supported by a hydrogen bond involving main chain atoms. Rab primary structure analysis revealed the presence of a Rab C-terminus characteristic sequence (AXA box), with two conserved aliphatic amino acid residues (Val191 and Leu193). Mutations of one of these residues induce a decrease of Rab affinity to GDI. Therefore, the AXA box contributes to increase Rab binding affinity to GDI upon complex formation.

Finally, there is a highly conserved region in the CCR (residues 225-228) named the <scene name='Sandbox_208/Residues_225-228_ccr/1'>mobile effector loop (MEL)</scene>. This part of the CCR directs GDI to the membrane and regulated the ability of GDI to retrieve Rab to the cytosol.

Finally, there is a highly conserved region in the CCR (residues 225-228) named the <scene name='Sandbox_208/Residues_225-228_ccr/2'>mobile effector loop (MEL)</scene>. This part of the CCR directs GDI to the membrane and regulated the ability of GDI to retrieve Rab to the cytosol.

*'''Domain II of GDI or Lipid Binding Site''': Domain II is rich in α helices. Helices D, E and H form a prenyl lipid binding pocket. <scene name='Sandbox_208/Lys145/1'>Lys145</scene> may play an important role in the lipid-binding cavity formation by functioning a spreader that keeps separated helices D and E. The GDI lipid binding pocket can adopt two different conformations, one being the open form when a lipid bound and the other being closed when neither lipid nor Rab is bound. A well ordered hydrophobic core stabilizes α helices D, E, F, G an H in a tighly packed state. This corresponds to the closed conformations of the GDI lipid binding site.

*'''Domain II of GDI or Lipid Binding Site''': Domain II is rich in α helices. Helices D, E and H form a prenyl lipid binding pocket. <scene name='Sandbox_208/Lys145/2'>Lys145</scene> may play an important role in the lipid-binding cavity formation by functioning a spreader that keeps separated helices D and E. The GDI lipid binding pocket can adopt two different conformations, one being the open form when a lipid bound and the other being closed when neither lipid nor Rab is bound. A well ordered hydrophobic core stabilizes α helices D, E, F, G an H in a tighly packed state. This corresponds to the closed conformations of the GDI lipid binding site.

When GDI and Rab bind together, the vast majority of domain II retains its structure. However, there is a rearrangement in α helices, exposing a part of the hydrophobic core residues and forming a hydrophobic cleft on the GDI surface. Interactions between Rab and GDI via the CCR and RBP induce the lipid pocket opening.

Both geranylgeranyl (GG) moities are located in the lipid binding site on top of each other. In this arrangement, the first bent lipid (GG1) protrudes into the core of domain II, anchoring to the lipid binding site thanks to the GDI residues <scene name='Sandbox_208/Gg1/1'>Val127, Pro128, Ala129, Ala134, Leu139, Met140, Met148, Leu152, Phe192, Met197, Cys221, Val224 and Ala225</scene>.

Both geranylgeranyl (GG) moities are located in the lipid binding site on top of each other. In this arrangement, the first bent lipid (GG1) protrudes into the core of domain II, anchoring to the lipid binding site thanks to the GDI residues <scene name='Sandbox_208/Gg1/2'>Val127, Pro128, Ala129, Ala134, Leu139, Met140, Met148, Leu152, Phe192, Met197, Cys221, Val224 and Ala225</scene>.

The second geranylgeranyl group (GG2) is located on the surface and it is aligned between helices D and E. Its binding site involves only seven hydrophobic amino acids: <scene name='Sandbox_208/Gg2/1'>Met148, Leu152, Ile155, Ile193, Trp200, Tyr205 and Leu218</scene>. GG2 forms a lid shielding a large part of the buried GG1 from the solvent. The environnement of GG2 is more hydrophilic than of the buried lipid.

The second geranylgeranyl group (GG2) is located on the surface and it is aligned between helices D and E. Its binding site involves only seven hydrophobic amino acids: <scene name='Sandbox_208/Gg2/2'>Met148, Leu152, Ile155, Ile193, Trp200, Tyr205 and Leu218</scene>. GG2 forms a lid shielding a large part of the buried GG1 from the solvent. The environnement of GG2 is more hydrophilic than of the buried lipid.

GDIs have functional specificity for a particular Rab. Both yeast and mammalians GDIs contains specific residues that contribute to the strength of their interaction with distinct Rab species.

Sandbox 208: Difference between revisions

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@@ Line 42: / Line 42: @@
 *'''GDI-Rab Binding Platform (RBP)''', with β strands e1 and e3 and helix C, which form a separate binding site. This platform is located in domain I and interacts with the globular part of the Rab molecule. The RabGDI binding epitope contains a great number of conserved residues on Rab: Ile41, Gly42, Asp/Glu44 and Phe45 from Switch I; Trp62, Asp63, Ala65, Gln67, Phe/Tyr70, Thr/Ala72, Thr74, Ser/Thr75, Ser/Ala76 and Arg79 from Switch II. More precisely, the RBP is an essential structural element which form a great number of interactions with the C-terminus and Switch I of Rab. Three additional invariable residues are located on RBP, and form hydrogen bonds with the switch I region and the C-terminus of Rab.
-*'''GDI C-terminus Coordinating Region (CCR) or C-terminus Binding Region (CBR)'''. The CBR represents a hydrophobic cavity on the GDI surface. In fact, this region is located in the cleft between domain I and domain II. It is formed by <scene name='Sandbox_208/Residues_93-112_domain_i/1'>residues 93-112</scene> from domain I and <scene name='Sandbox_208/Residues_226-235_domain_ii/1'>residues 226-235</scene> from domain II. The CBR coordinates the flexible extended C-terminus of Rab. In most cases, the CBR is occupied by side chains of hydrophobic residues of the Rab C-terminus tail. Hydrophobic contacts between GDI and Rab are supported by a hydrogen bond involving main chain atoms. Rab primary structure analysis revealed the presence of a Rab C-terminus characteristic sequence (AXA box), with two conserved aliphatic amino acid residues (Val191 and Leu193). Mutations of one of these residues induce a decrease of Rab affinity to GDI. Therefore, the AXA box contributes to increase Rab binding affinity to GDI upon complex formation.
+*'''GDI C-terminus Coordinating Region (CCR) or C-terminus Binding Region (CBR)'''. The CBR represents a hydrophobic cavity on the GDI surface. In fact, this region is located in the cleft between domain I and domain II. It is formed by <scene name='Sandbox_208/Residues_93-112_domain_i/2'>residues 93-112</scene> from domain I and <scene name='Sandbox_208/Residues_226-235_domain_ii/2'>residues 226-235</scene> from domain II. The CBR coordinates the flexible extended C-terminus of Rab. In most cases, the CBR is occupied by side chains of hydrophobic residues of the Rab C-terminus tail. Hydrophobic contacts between GDI and Rab are supported by a hydrogen bond involving main chain atoms. Rab primary structure analysis revealed the presence of a Rab C-terminus characteristic sequence (AXA box), with two conserved aliphatic amino acid residues (Val191 and Leu193). Mutations of one of these residues induce a decrease of Rab affinity to GDI. Therefore, the AXA box contributes to increase Rab binding affinity to GDI upon complex formation.
-Finally, there is a highly conserved region in the CCR (residues 225-228) named the <scene name='Sandbox_208/Residues_225-228_ccr/1'>mobile effector loop (MEL)</scene>. This part of the CCR directs GDI to the membrane and regulated the ability of GDI to retrieve Rab to the cytosol.
+Finally, there is a highly conserved region in the CCR (residues 225-228) named the <scene name='Sandbox_208/Residues_225-228_ccr/2'>mobile effector loop (MEL)</scene>. This part of the CCR directs GDI to the membrane and regulated the ability of GDI to retrieve Rab to the cytosol.
-*'''Domain II of GDI or Lipid Binding Site''': Domain II is rich in α helices. Helices D, E and H form a prenyl lipid binding pocket. <scene name='Sandbox_208/Lys145/1'>Lys145</scene> may play an important role in the lipid-binding cavity formation by functioning a spreader that keeps separated helices D and E. The GDI lipid binding pocket can adopt two different conformations, one being the open form when a lipid bound and the other being closed when neither lipid nor Rab is bound. A well ordered hydrophobic core stabilizes α helices D, E, F, G an H in a tighly packed state. This corresponds to the closed conformations of the GDI lipid binding site.
+*'''Domain II of GDI or Lipid Binding Site''': Domain II is rich in α helices. Helices D, E and H form a prenyl lipid binding pocket. <scene name='Sandbox_208/Lys145/2'>Lys145</scene> may play an important role in the lipid-binding cavity formation by functioning a spreader that keeps separated helices D and E. The GDI lipid binding pocket can adopt two different conformations, one being the open form when a lipid bound and the other being closed when neither lipid nor Rab is bound. A well ordered hydrophobic core stabilizes α helices D, E, F, G an H in a tighly packed state. This corresponds to the closed conformations of the GDI lipid binding site.
 When GDI and Rab bind together, the vast majority of domain II retains its structure. However, there is a rearrangement in α helices, exposing a part of the hydrophobic core residues and forming a hydrophobic cleft on the GDI surface. Interactions between Rab and GDI via the CCR and RBP induce the lipid pocket opening.
-Both geranylgeranyl (GG) moities are located in the lipid binding site on top of each other. In this arrangement, the first bent lipid (GG1) protrudes into the core of domain II, anchoring to the lipid binding site thanks to the GDI residues <scene name='Sandbox_208/Gg1/1'>Val127, Pro128, Ala129, Ala134, Leu139, Met140, Met148, Leu152, Phe192, Met197, Cys221, Val224 and Ala225</scene>.
+Both geranylgeranyl (GG) moities are located in the lipid binding site on top of each other. In this arrangement, the first bent lipid (GG1) protrudes into the core of domain II, anchoring to the lipid binding site thanks to the GDI residues <scene name='Sandbox_208/Gg1/2'>Val127, Pro128, Ala129, Ala134, Leu139, Met140, Met148, Leu152, Phe192, Met197, Cys221, Val224 and Ala225</scene>.
-The second geranylgeranyl group (GG2) is located on the surface and it is aligned between helices D and E. Its binding site involves only seven hydrophobic amino acids: <scene name='Sandbox_208/Gg2/1'>Met148, Leu152, Ile155, Ile193, Trp200, Tyr205 and Leu218</scene>. GG2 forms a lid shielding a large part of the buried GG1 from the solvent. The environnement of GG2 is more hydrophilic than of the buried lipid.
+The second geranylgeranyl group (GG2) is located on the surface and it is aligned between helices D and E. Its binding site involves only seven hydrophobic amino acids: <scene name='Sandbox_208/Gg2/2'>Met148, Leu152, Ile155, Ile193, Trp200, Tyr205 and Leu218</scene>. GG2 forms a lid shielding a large part of the buried GG1 from the solvent. The environnement of GG2 is more hydrophilic than of the buried lipid.
 GDIs have functional specificity for a particular Rab. Both yeast and mammalians GDIs contains specific residues that contribute to the strength of their interaction with distinct Rab species.