High-resolution crystal structure of S. cerevisiae Ypt51(ΔC15)-GppNHp, a small GTP-binding protein involved in regulation of endocytosis

• Published in: Journal of molecular biology 2000-04, Vol.298 (1), p.111-121
• Main Authors: Esters, Heike, Alexandrov, Kirill, Constantinescu, Alexandru-Tudor, Goody, Roger S, Scheidig, Axel J
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Animals; binding proteins; Binding Sites; crystal structure; Crystallography, X-Ray; crystals; Endocytosis; Enzyme Activation; GTP-binding protein; guanosine triphosphate; Guanylyl Imidodiphosphate - metabolism; Hydrogen Bonding; Hydrolysis; hydrophobicity; Magnesium - metabolism; Models, Molecular; molecular conformation; Molecular Sequence Data; Nickel - metabolism; pdb/1ek0; Protein Isoforms - chemistry; Protein Isoforms - genetics; Protein Structure, Tertiary; Proto-Oncogene Proteins p21(ras) - chemistry; rab GTP-Binding Proteins - chemistry; rab GTP-Binding Proteins - genetics; rab GTP-Binding Proteins - metabolism; rab3A GTP-Binding Protein - chemistry; Rats; Saccharomyces cerevisiae; Saccharomyces cerevisiae - chemistry; Saccharomyces cerevisiae - cytology; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae Proteins; Sequence Alignment; Sequence Deletion; Structure-Activity Relationship; vesicular transport; Vps21; X-ray diffraction; Ypt51; Ypt51p protein
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1006/jmbi.2000.3645

Ypt/Rab proteins are membrane-associated small GTP-binding proteins which play a central role in the coordination, activation and regulation of vesicle-mediated transport in eukaryotic cells. We present the 1.5 Å high-resolution crystal structure of Ypt51 in its active, GppNHp-bound conformation. Ypt51 is an important regulator involved in the endocytic membrane traffic of Saccharomyces cerevisiae. The structure reveals small but significant structural differences compared with H-Ras p21. The effector loop and the catalytic loop are well defined and stabilized by extensive hydrophobic interactions. The switch I and switch II regions form a well-defined epitope for hypothetical effector protein binding. Sequence comparisons between the different isoforms Ypt51, Ypt52 and Ypt53 provide the first insights into determinants for specific effector binding and for fine-tuning of the intrinsic GTP-hydrolysis rate.