3CPJ

Crystal structure of Ypt31 in complex with yeast Rab-GDI

Summary for 3CPJ

• Entry DOI: 10.2210/pdb3cpj/pdb
• Related: 3CPH 3CPI
• Descriptor: Rab GDP-dissociation inhibitor, GTP-binding protein YPT31/YPT8, CHLORIDE ION, ... (6 entities in total)
• Functional Keywords: rab gtpase, prenylation, vesicular transport, acetylation, golgi apparatus, gtp-binding, lipoprotein, membrane, nucleotide-binding, protein transport, cytoplasm, gtpase activation, phosphoprotein
• Biological source: Saccharomyces cerevisiae (baker's yeast); More
• Cellular location: Golgi apparatus membrane; Lipid-anchor: P39958; Cytoplasm: P38555
• Total number of polymer chains: 2
• Total formula weight: 76317.66

Authors

Kravchenko, S.,Ignatev, A.,Goody, R.S.,Rak, A.,Pylypenko, O. (deposition date: 2008-03-31, release date: 2008-05-06, Last modification date: 2023-11-01)

Primary citation

Ignatev, A.,Kravchenko, S.,Rak, A.,Goody, R.S.,Pylypenko, O.
A structural model of the GDP dissociation inhibitor rab membrane extraction mechanism.
J.Biol.Chem., 283:18377-18384, 2008

PubMed Abstract: Rab GDP dissociation inhibitors (GDI)-facilitated extraction of prenylated Rab proteins from membranes plays an important role in vesicular membrane trafficking. The investigated thermodynamic properties of yeast Rab.GDI and Rab.MRS6 complexes demonstrated differences in the Rab binding properties of the closely related Rab GDI and MRS6 proteins, consistent with their functional diversity. The importance of the Rab C terminus and its prenylation for GDI/MRS6 binding was demonstrated using both biochemical and structural data. The presented structures of the apo-form yeast Rab GDI and its two complexes with unprenylated Rab proteins, together with the earlier published structures of the prenylated Ypt1.GDI, provide evidence of allosteric regulation of the GDI lipid binding site opening, which plays a key role in the proposed mechanism of GDI-mediated Rab extraction. We suggest a model for the interaction of GDI with prenylated Rab proteins that incorporates a stepwise increase in affinity as the three different partial interactions are successively formed.

PubMed: 18426803
DOI: 10.1074/jbc.M709718200

Experimental method

X-RAY DIFFRACTION (2.35 Å)