PDBsum entry 1ocs

Sorting protein

PDB id: 1ocs

Contents

Protein chain

132 a.a. *

Ligands

GOL

Waters ×63

* Residue conservation analysis

PDB id:

1ocs

Name:

Sorting protein

Title:

Crystal structure of the yeast px-doamin protein grd19p (sorting nexin3) complexed to phosphatidylinosytol-3-phosphate.

Structure:

Sorting nexin grd19. Chain: a. Fragment: px-domain, residues 1-162. Engineered: yes. Other_details: cysteine a91 chemically modified by beta mercapto- ethanol

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: s288c. Expressed in: escherichia coli. Expression_system_taxid: 469008. Other_details: cloned gene

Resolution:

2.03Å R-factor: 0.217 R-free: 0.247

Authors:

C.Z.Zhou,I.Li De La Sierra-Gallay,S.Cheruel,B.Collinet,P.Minard, K.Blondeau,G.Henkes,R.Aufrere,N.Leulliot,M.Graille,I.Sorel, P.Savarin,F.De La Torre,A.Poupon,J.Janin,H.Van Tilbeurgh

Key ref:

C.Z.Zhou et al. (2003). Crystal structure of the yeast Phox homology (PX) domain protein Grd19p complexed to phosphatidylinositol-3-phosphate. J Biol Chem, 278, 50371-50376. PubMed id: 14514667 DOI: 10.1074/jbc.M304392200

Date:

10-Feb-03 Release date: 12-Dec-03

Protein chain

Q08826  (SNX3_YEAST) -  Sorting nexin-3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 162 a.a.

Struc: 132 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1074/jbc.M304392200

J Biol Chem 278:50371-50376 (2003)

PubMed id: 14514667

Crystal structure of the yeast Phox homology (PX) domain protein Grd19p complexed to phosphatidylinositol-3-phosphate.

C.Z.Zhou, I.L.de La Sierra-Gallay, S.Quevillon-Cheruel, B.Collinet, P.Minard, K.Blondeau, G.Henckes, R.Aufrère, N.Leulliot, M.Graille, I.Sorel, P.Savarin, F.de la Torre, A.Poupon, J.Janin, H.van Tilbeurgh.

ABSTRACT

Phox homology (PX) domains have been recently identified in a number of different proteins and are involved in various cellular functions such as vacuolar targeting and membrane protein trafficking. It was shown that these modules of about 130 amino acids specifically binding to phosphoinositides and that this interaction is crucial for their cellular function. The yeast genome contains 17 PX domain proteins. One of these, Grd19p, is involved in the localization of the late Golgi membrane proteins DPAP A and Kex2p. Grd19p consists of the PX domain with 30 extra residues at the N-terminal and is homologous to the functionally characterized human sorting nexin protein SNX3. We determined the 2.0 A crystal structure of Grd19p in the free form and in complex with d-myo-phosphatidylinositol 3-phosphate (diC4PtdIns(3)P), representing the first case of both free and ligand-bound conformations of the same PX module. The ligand occupies a well defined positively charged binding pocket at the interface between the beta-sheet and alpha-helical parts of the molecule. The structure of the free and bound protein are globally similar but show some significant differences in a region containing a polyproline peptide and a putative membrane attachment site.

Selected figure(s)

Figure 3.
FIG. 3. A, stereo view of an omitted F[o] - F[c] electron density map covering the bound diC4PtdIns(3)P, contoured at 3 . B, overall view of binding of diC4PtdIns(3)P to Grd19p. Helices are colored yellow, strands green, and loop connections purple. The ligand is represented in sticks (gray, carbon; red, oxygen; and pink, phosphate). Some of the secondary structure elements (Fig. 1) are labeled. C, detailed stereo view of diC4PtdIns(3)P binding to Grd19p (yellow, carbon atoms; green, phosphate; red, oxygen; and blue, nitrogen). Positions of the phosphate groups of the ligand on the 1- and 3-OH position are labeled as P1 and P3, respectively.

Figure 4.
FIG. 4. A, stereo view of the superposition of the ligand-bound (C atoms in yellow) and free form (C atoms in wheat) of Grd19p. Residues in a radius of 5 Å around the bound ligand are represented. B, stereo view of the superposition of the ligand-binding sites of Grd19p and p40^phox. Grd19p, same color code as Fig. 4A. p40^phox has carbon atoms in green. Only the Grd19p residues are labeled.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 50371-50376) copyright 2003.

Figures were selected by an automated process.