PDBsum entry 2eqb

Endocytosis/exocytosis

PDB id: 2eqb

Contents

Protein chains

171 a.a. *

93 a.a. *

Ligands

PO4 ×2

Waters ×114

* Residue conservation analysis

PDB id:

2eqb

Name:

Endocytosis/exocytosis

Title:

Crystal structure of the rab gtpase sec4p, the sec2p gef domain, and phosphate complex

Structure:

Ras-related protein sec4. Chain: a. Fragment: residues 19-187. Synonym: suppressor of rho3 protein 6, rab gtpase sec4p. Engineered: yes. Rab guanine nucleotide exchange factor sec2. Chain: b, c. Fragment: gef domain, residues 51-142. Synonym: gdp-gtp exchange factor sec2.

Source:

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

Resolution:

2.70Å R-factor: 0.273 R-free: 0.298

Authors:

Y.Sato,S.Fukai,R.Ishitani,O.Nureki

Key ref:

Y.Sato et al. (2007). Crystal structure of the Sec4p{middle dot}Sec2p complex in the nucleotide exchanging intermediate state. Proc Natl Acad Sci U S A, 104, 8305-8310. PubMed id: 17488829 DOI: 10.1073/pnas.0701550104

Date:

30-Mar-07 Release date: 22-May-07

Protein chain

P07560  (SEC4_YEAST) -  Ras-related protein SEC4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 215 a.a.

Struc: 171 a.a.*

Protein chains

P17065  (SEC2_YEAST) -  Rab guanine nucleotide exchange factor SEC2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 759 a.a.

Struc: 93 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C: E.C.?

DOI no: 10.1073/pnas.0701550104

Proc Natl Acad Sci U S A 104:8305-8310 (2007)

PubMed id: 17488829

Crystal structure of the Sec4p{middle dot}Sec2p complex in the nucleotide exchanging intermediate state.

Y.Sato, S.Fukai, R.Ishitani, O.Nureki.

ABSTRACT

Vesicular transport during exocytosis is regulated by Rab GTPase (Sec4p in yeast), which is activated by a guanine nucleotide exchange factor (GEF) called Sec2p. Here, we report the crystal structure of the Sec2p GEF domain in a complex with the nucleotide-free Sec4p at 2.7 A resolution. Upon complex formation, the Sec2p helices approach each other, flipping the side chain of Phe-109 toward Leu-104 and Leu-108 of Sec2p. These three residues provide a hydrophobic platform to attract the side chains of Phe-49, Ile-53, and Ile-55 in the switch I region as well as Phe-57 and Trp-74 in the interswitch region of Sec4p. Consequently, the switch I and II regions are largely deformed, to create a flat hydrophobic interface that snugly fits the surface of the Sec2p coiled coil. These drastic conformational changes disrupt the interactions between switch I and the bound guanine nucleotide, which facilitates the GDP release. Unlike the recently reported 3.3 A structure of the Sec4p.Sec2p complex, our structure contains a phosphate ion bound to the P-loop, which may represent an intermediate state of the nucleotide exchange reaction.

Selected figure(s)

Figure 2.
Fig. 2. Sec4p·Sec2p binding interface. (a) Stereoview of the detailed Sec4p·Sec2p binding interface. The coloring scheme is the same as in Fig. 1b. Hydrogen bonds are shown by dotted orange lines. (b) Schematic representation of the Sec4p·Sec2p interface. The hydrogen bonds (with a 3.4 Å cutoff) are displayed as solid orange lines. The hydrophobic contacts (with a 4.0 Å cutoff) are displayed as dotted green lines. The labels of the switch I, interswitch, switch II, and other regions of Sec4p are highlighted in cyan, brown, pink, and gray, respectively. The labels of the sharply and moderately bent helices of Sec2p are highlighted in yellow and green, respectively.

Figure 4.
Fig. 4. Comparison of the Sec4p·GDP and Sec2p-bound Sec4p structures. (a) Comparison of the overall structures of Sec4p·GDP and Sec2p-bound Sec4p. Sec4p·GDP was superposed onto Sec4p in the Sec4p·Sec2p·phosphate complex, except for the residues 42–47, and the switch I (residues 48–56) and switch II (residues 76–93) regions. Sec4p·GDP is colored yellow, and Sec4p in the Sec4p·Sec2p·phosphate complex is colored as in Fig. 1b. The carbon atoms of the Sec4p-bound GDP are green, and the bound cobalt ion is yellow. (b) Comparison of the Sec2p binding region in the Sec4p·GDP and Sec2p-bound Sec4p structures. Coloring schemes are the same as in a. Dotted black arrows indicate positional changes of the amino acid residues.

Figures were selected by an automated process.