High-resolution crystal structure of S. cerevisiae Ypt51(DeltaC15)-GppNHp, a small GTP-binding protein involved in regulation of endocytosis.
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 A 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.
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Abteilung für Physikalische Biochemie, Max-Planck Institut für molekulare Physiologie, Otto-Hahn-Strasse 11, Dortmund, 44227, Germany.
Alexandrov
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K
Constantinescu
A T
AT
Goody
R S
RS
Scheidig
A J
AJ
D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004705:Endocytosis; D004789:Enzyme Activation; D006165:Guanylyl Imidodiphosphate / Q000378:metabolism*; D006860:Hydrogen Bonding; D006868:Hydrolysis; D008274:Magnesium / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009532:Nickel / Q000378:metabolism; D020033:Protein Isoforms / Q000737:chemistry / Q000235:genetics; D017434:Protein Structure, Tertiary; D016283:Proto-Oncogene Proteins p21(ras) / Q000737:chemistry; D051381:Rats; D012441:Saccharomyces cerevisiae / Q000737:chemistry* / Q000166:cytology / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins; D016415:Sequence Alignment; D017384:Sequence Deletion; D013329:Structure-Activity Relationship; D020691:rab GTP-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D020826:rab3A GTP-Binding Protein / Q000737:chemistry
D020033:Protein Isoforms; D029701:Saccharomyces cerevisiae Proteins; D006165:Guanylyl Imidodiphosphate; D009532:Nickel; C086866:VPS21 protein, S cerevisiae; D016283:Proto-Oncogene Proteins p21(ras); D020691:rab GTP-Binding Proteins; D020826:rab3A GTP-Binding Protein; D008274:Magnesium