PDBsum entry 1mqs

Endocytosis/exocytosis

PDB id: 1mqs

Contents

Protein chains

588 a.a. *

26 a.a. *

Waters ×20

* Residue conservation analysis

PDB id:

1mqs

Name:

Endocytosis/exocytosis

Title:

Crystal structure of sly1p in complex with an n-terminal peptide of sed5p

Structure:

Sly1 protein. Chain: a. Synonym: sly1p. Engineered: yes. Integral membrane protein sed5. Chain: b. Synonym: sed5p. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

3.00Å R-factor: 0.257 R-free: 0.290

Authors:

A.Bracher,W.Weissenhorn

Key ref:

A.Bracher and W.Weissenhorn (2002). Structural basis for the Golgi membrane recruitment of Sly1p by Sed5p. EMBO J, 21, 6114-6124. PubMed id: 12426383 DOI: 10.1093/emboj/cdf608

Date:

17-Sep-02 Release date: 20-Nov-02

Protein chain

P22213  (SLY1_YEAST) -  Protein SLY1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 666 a.a.

Struc: 588 a.a.

Protein chain

Q01590  (SED5_YEAST) -  Integral membrane protein SED5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 340 a.a.

Struc: 26 a.a.

DOI no: 10.1093/emboj/cdf608

EMBO J 21:6114-6124 (2002)

PubMed id: 12426383

Structural basis for the Golgi membrane recruitment of Sly1p by Sed5p.

A.Bracher, W.Weissenhorn.

ABSTRACT

Cytosolic Sec1/munc18-like proteins (SM proteins) are recruited to membrane fusion sites by interaction with syntaxin-type SNARE proteins, constituting indispensable positive regulators of intracellular membrane fusion. Here we present the crystal structure of the yeast SM protein Sly1p in complex with a short N-terminal peptide derived from the Golgi-resident syntaxin Sed5p. Sly1p folds, similarly to neuronal Sec1, into a three-domain arch-shaped assembly, and Sed5p interacts in a helical conformation predominantly with domain I of Sly1p on the opposite site of the nSec1/syntaxin-1-binding site. Sequence conservation of the major interactions suggests that homologues of Sly1p as well as the paralogous Vps45p group bind their respective syntaxins in the same way. Furthermore, we present indirect evidence that nSec1 might be able to contact syntaxin 1 in a similar fashion. The observed Sly1p-Sed5p interaction mode therefore indicates how SM proteins can stay associated with the assembling fusion machinery in order to participate in late fusion steps.

Selected figure(s)

Figure 1.
Figure 1 Close-ups of Sly1p−Sed5p interactions. (A) Stereo diagram of the experimental electron density map of the Sly1p−Sed5p complex. The region shows the conserved Sly1p hydrophobic pocket (residues Leu137, Leu140, Ala141, Ile153 and Val156) that accommodates the Sed5p key residue Phe10. The map is contoured at 0.8 . (B) Hydrogen bond network at the interface of Sly1p and Sed5p. Residues 1−9 of Sed5p are shown as a ball-and-stick model in yellow; residues 131−134, 138 and 156−160 of Sly1p are shown in grey. Oxygen and nitrogen atoms are shown in red and blue, respectively. Hydrogen bonds are indicated as dashed lines. Note that the region comprising residues 10−21 of Sed5p is involved in hydrophobic interactions only. (C) Superposition of domain I of Sly1p in complex with Sed5p with the corresponding region in s-Sec1 including a helical segment from a neighbouring molecule forming a crystal contact (pdb code 1FVH). The r.m.s.d. for the fragments shown is 1.34 Å within 127 residues (35 identical). The peptide backbones are shown as C[ ]-traces. The colouring scheme is as follows: Sly1p, yellow; Sed5p, red; s-Sec1 domain I, white; and s-Sec1 residues 321−332, mimicking the Sed5p helical interaction, blue. N- and C-termini are indicated.

Figure 5.
Figure 5 Surface conservation of Sly1p homologues. The homology score for an alignment of Sly1p homologue sequences was plotted on to the surface of Sly1p using a scale from green (identical) to white (no conservation). Coils denote the backbone of Sed5p (yellow) and of an insertion containing helices 20 and 21 (red). (A) The orientation is similar to Figure 2. (B) Orientation after an 150° rotation around the vertical axis. Some conserved residues are indicated for orientation.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2002, 21, 6114-6124) copyright 2002.

Figures were selected by an automated process.