Components of Coated Vesicles and Nuclear Pore Complexes Share a Common Molecular Architecture

• DOI: 10.1371/journal.pbio.0020380
• Publication Date: 2004-11-02T23:23:46Z
• Authors: Damien Devos; Svetlana Dokudovs...; Frank Alber; Rosemary Williams; Brian T Chait; Andrej Sali; Michael P Rout
• Keywords: Models, Molecular; 0301 basic medicine; 570; Protein Structure; Secondary; Protein Folding; Saccharomyces cerevisiae Proteins; Biomedical and clinical sciences; Evolution; QH301-705.5; Nuclear Envelope; Protein Conformation; 1.1 Normal biological development and functioning; Molecular Sequence Data; Coated Vesicles; Saccharomyces cerevisiae; Medical and Health Sciences; Biochemistry; Models, Biological; Protein Structure, Secondary; Evolution, Molecular; Fungal Proteins; 03 medical and health sciences; veterinary and food sciences; Underpinning research; Models; Biology (General); Cell Nucleus; Agricultural; Agricultural and Veterinary Sciences; Cell Membrane; Molecular; Chromosome Mapping; Computational Biology; Biological Transport; Biological Sciences; 540; Biological; Protein Structure, Tertiary; Nuclear Pore Complex Proteins; Biological sciences; Nuclear Pore; Biochemistry and Cell Biology; Generic health relevance; Tertiary; Developmental Biology; Research Article

Numerous features distinguish prokaryotes from eukaryotes, chief among which are the distinctive internal membrane systems of eukaryotic cells. These membrane systems form elaborate compartments and vesicular trafficking pathways, and sequester the chromatin within the nuclear envelope. The nuclear pore complex is the portal that specifically mediates macromolecular trafficking across the nuclear envelope. Although it is generally understood that these internal membrane systems evolved from specialized invaginations of the prokaryotic plasma membrane, it is not clear how the nuclear pore complex could have evolved from organisms with no analogous transport system. Here we use computational and biochemical methods to perform a structural analysis of the seven proteins comprising the yNup84/vNup107-160 subcomplex, a core building block of the nuclear pore complex. Our analysis indicates that all seven proteins contain either a beta-propeller fold, an alpha-solenoid fold, or a distinctive arrangement of both, revealing close similarities between the structures comprising the yNup84/vNup107-160 subcomplex and those comprising the major types of vesicle coating complexes that maintain vesicular trafficking pathways. These similarities suggest a common evolutionary origin for nuclear pore complexes and coated vesicles in an early membrane-curving module that led to the formation of the internal membrane systems in modern eukaryotes.