Structural basis for the binding of tryptophan-based motifs by δ-COP. Author Richard Suckling, Pak Poon, Sophie Travis, Irina Majoul, Frederick Hughson, Philip Evans, Rainer Duden, David Owen Publication Year 2015 Type Journal Article Abstract Coatomer consists of two subcomplexes: the membrane-targeting, ADP ribosylation factor 1 (Arf1):GTP-binding βγδζ-COP F-subcomplex, which is related to the adaptor protein (AP) clathrin adaptors, and the cargo-binding αβ'ε-COP B-subcomplex. We present the structure of the C-terminal μ-homology domain of the yeast δ-COP subunit in complex with the WxW motif from its binding partner, the endoplasmic reticulum-localized Dsl1 tether. The motif binds at a site distinct from that used by the homologous AP μ subunits to bind YxxΦ cargo motifs with its two tryptophan residues sitting in compatible pockets. We also show that the Saccharomyces cerevisiae Arf GTPase-activating protein (GAP) homolog Gcs1p uses a related WxxF motif at its extreme C terminus to bind to δ-COP at the same site in the same way. Mutations designed on the basis of the structure in conjunction with isothermal titration calorimetry confirm the mode of binding and show that mammalian δ-COP binds related tryptophan-based motifs such as that from ArfGAP1 in a similar manner. We conclude that δ-COP subunits bind Wxn(1-6)[WF] motifs within unstructured regions of proteins that influence the lifecycle of COPI-coated vesicles; this conclusion is supported by the observation that, in the context of a sensitizing domain deletion in Dsl1p, mutating the tryptophan-based motif-binding site in yeast causes defects in both growth and carboxypeptidase Y trafficking/processing. Keywords Protein Binding, Protein Structure, Tertiary, DNA-Binding Proteins, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Amino Acid Motifs, COP-Coated Vesicles, Calorimetry, Indirect, Cathepsin A, Coatomer Protein, GTPase-Activating Proteins, Tryptophan Journal Proc Natl Acad Sci U S A Volume 112 Issue 46 Pages 14242-7 Date Published 2015 Nov 17 ISSN Number 1091-6490 DOI 10.1073/pnas.1506186112 Alternate Journal Proc Natl Acad Sci U S A PMCID PMC4655537 PMID 26578768 PubMedPubMed CentralGoogle ScholarBibTeXEndNote X3 XML