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Crystal structure of the Sec4p·Sec2p complex in the nucleotide exchanging intermediate state
- Sato, Yusuke, Fukai, Shuya, Ishitani, Ryuichiro, Nureki, Osamu
- Proceedings of the National Academy of Sciences of the United States of America 2007 v.104 no.20 pp. 8305-8310
- crystal structure, exocytosis, guanine nucleotides, guanosinetriphosphatase, hydrophobicity, phosphates, regulatory proteins, yeasts
- Vesicular transport during exocytosis is regulated by Rab GTPase (Sec4p in yeast), which is activated by a guanine nucleotide exchange factor (GEF) called Sec2p. Here, we report the crystal structure of the Sec2p GEF domain in a complex with the nucleotide-free Sec4p at 2.7 Å resolution. Upon complex formation, the Sec2p helices approach each other, flipping the side chain of Phe-109 toward Leu-104 and Leu-108 of Sec2p. These three residues provide a hydrophobic platform to attract the side chains of Phe-49, Ile-53, and Ile-55 in the switch I region as well as Phe-57 and Trp-74 in the interswitch region of Sec4p. Consequently, the switch I and II regions are largely deformed, to create a flat hydrophobic interface that snugly fits the surface of the Sec2p coiled coil. These drastic conformational changes disrupt the interactions between switch I and the bound guanine nucleotide, which facilitates the GDP release. Unlike the recently reported 3.3 Å structure of the Sec4p·Sec2p complex, our structure contains a phosphate ion bound to the P-loop, which may represent an intermediate state of the nucleotide exchange reaction.