Sandbox 208: Difference between revisions
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Both REP and GDI are considered as Rab molecular [http://http://en.wikipedia.org/wiki/Chaperone_(protein) chaperones]. They have similar organization, in particular, their Rab binding interface which is well conserved. | Both REP and GDI are considered as Rab molecular [http://http://en.wikipedia.org/wiki/Chaperone_(protein) chaperones]. They have similar organization, in particular, their Rab binding interface which is well conserved. | ||
=Structure= | =Structure<ref>PMID: 18426803</ref>= | ||
<StructureSection load='3cpi' size='550' side='right' caption='Assymetric unit of Rab-GDP Dissociation Inhibitor (PDB entry [[3cpi]])' scene=''> | <StructureSection load='3cpi' size='550' side='right' caption='Assymetric unit of Rab-GDP Dissociation Inhibitor (PDB entry [[3cpi]])' scene=''> | ||
3CPI is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CPI OCA]. | 3CPI is a 2 chains structure of sequences from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CPI OCA]. | ||
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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. | 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 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. | 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. | ||