PDBsum entry 1vfy

Transport protein

PDB id: 1vfy

Contents

Protein chain

67 a.a. *

Metals

_ZN ×2

Waters ×109

* Residue conservation analysis

PDB id:

1vfy

Name:

Transport protein

Title:

Phosphatidylinositol-3-phosphate binding fyve domain of vps27p protein from saccharomyces cerevisiae

Structure:

Phosphatidylinositol-3-phosphate binding fyve domain of protein vps27. Chain: a. Fragment: 163-229, fyve domain. Engineered: yes. Mutation: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Cellular_location: cytoplasm, endosomal membranes. Gene: vps27. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Expression_system_variant: de3.

Resolution:

1.15Å R-factor: 0.174 R-free: 0.181

Authors:

J.H.Hurley,S.Misra

Key ref:

S.Misra and J.H.Hurley (1999). Crystal structure of a phosphatidylinositol 3-phosphate-specific membrane-targeting motif, the FYVE domain of Vps27p. Cell, 97, 657-666. PubMed id: 10367894 DOI: 10.1016/S0092-8674(00)80776-X

Date:

26-Apr-99 Release date: 06-May-99

Protein chain

P40343  (VPS27_YEAST) -  Vacuolar protein sorting-associated protein 27 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 622 a.a.

Struc: 67 a.a.*

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

DOI no: 10.1016/S0092-8674(00)80776-X

Cell 97:657-666 (1999)

PubMed id: 10367894

Crystal structure of a phosphatidylinositol 3-phosphate-specific membrane-targeting motif, the FYVE domain of Vps27p.

S.Misra, J.H.Hurley.

ABSTRACT

Phosphatidylinositol 3-phosphate regulates membrane trafficking and signaling pathways by interacting with the FYVE domains of target proteins. The 1.15 A structure of the Vps27p FYVE domain reveals two antiparallel beta sheets and an alpha helix stabilized by two Zn2+-binding clusters. The core secondary structures are similar to a rabphilin-3A Zn2+-binding domain and to the C1 and LIM domains. Phosphatidylinositol 3-phosphate binds to a pocket formed by the (R/K)(R/K)HHCR motif. A lattice contact shows how anionic ligands can interact with the phosphatidylinositol 3-phosphate-binding site. The tip of the FYVE domain has basic and hydrophobic surfaces positioned so that nonspecific interactions with the phospholipid bilayer can abet specific binding to phosphatidylinositol 3-phosphate.

Selected figure(s)

Figure 3.
Figure 3. Molecular Surface of the FYVE DomainThe surfaces are colored by (A) electrostatic potential, with saturating color at ±5 kT/e, and (B) residue type: hydrophobic, green; basic, blue; acidic, red; and uncharged polar, white. Surfaces were drawn and colored using GRASP ([21]). The upper figures show the protein in sagittal projection, looking into the putative PI3P-binding site. The membrane-proximal end of the protein is at the bottom. The lower figures depict a view from the membrane normal into the protein. The PI3P-binding site is at the top.

Figure 6.
Figure 6. Membrane Interaction ModelThe Vps27p FYVE domain, rabphilin-3A/Rab3A complex (Brünger et al., 1999), and the C1b domain of protein kinase Cδ ([64]), shown in the predicted membrane-bound orientation (sagittal projection). Orientations of rabphilin-3A/Rab3A and PKCδ-C1b are based on structural alignments with the Vps27p-FYVE. Hydrophobic ligands and residues that may be important for membrane interactions are shown. The membrane is divided according to the model of [60 and 58], which describes the distribution of lipid and protein functional groups within the bilayer. The interfacial region, containing water, lipid headgroups, glycerol, carbonyl, and methylene groups, constitutes the outer quarters of the membrane; the central half of the membrane is occupied by a hydrocarbon core, containing the lipid fatty acid chains. The interfacial zone of the membrane is depicted to scale with a thickness of 15 Å. We have inserted the proteins to reasonable depths in the membrane. The C-terminal end of the ordered part of the solved Rab3A structure is labeled; the C terminus of the full-length protein is geranyl geranylated. In the orientation shown, the Rab3A C terminus is near enough to the membrane surface that a covalently attached geranyl–geranyl moiety can penetrate into the membrane. Structures were drawn using Molscript and Raster3D.

The above figures are reprinted by permission from Cell Press: Cell (1999, 97, 657-666) copyright 1999.

Figures were selected by the author.