High-resolution crystal structure of S. cerevisiae Ypt51(DeltaC15)-GppNHp, a small GTP-binding protein involved in regulation of endocytosis

J Mol Biol. 2000 Apr 21;298(1):111-21. doi: 10.1006/jmbi.2000.3645.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Binding Sites
  • Crystallography, X-Ray
  • Endocytosis*
  • Enzyme Activation
  • Guanylyl Imidodiphosphate / metabolism*
  • Hydrogen Bonding
  • Hydrolysis
  • Magnesium / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Nickel / metabolism
  • Protein Isoforms / chemistry
  • Protein Isoforms / genetics
  • Protein Structure, Tertiary
  • Proto-Oncogene Proteins p21(ras) / chemistry
  • Rats
  • Saccharomyces cerevisiae / chemistry*
  • Saccharomyces cerevisiae / cytology
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae Proteins*
  • Sequence Alignment
  • Sequence Deletion
  • Structure-Activity Relationship
  • rab GTP-Binding Proteins / chemistry*
  • rab GTP-Binding Proteins / genetics
  • rab GTP-Binding Proteins / metabolism*
  • rab3A GTP-Binding Protein / chemistry

Substances

  • Protein Isoforms
  • Saccharomyces cerevisiae Proteins
  • Guanylyl Imidodiphosphate
  • Nickel
  • VPS21 protein, S cerevisiae
  • Proto-Oncogene Proteins p21(ras)
  • rab GTP-Binding Proteins
  • rab3A GTP-Binding Protein
  • Magnesium

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