PDBsum entry 2bcg

Protein transport

PDB id: 2bcg

Contents

Protein chains

442 a.a. *

194 a.a. *

Ligands

GER ×2

GDP

TRS

Metals

_MG

Waters ×923

* Residue conservation analysis

PDB id:

2bcg

Name:

Protein transport

Title:

Structure of doubly prenylated ypt1:gdi complex

Structure:

Secretory pathway gdp dissociation inhibitor. Chain: g. Fragment: rabgdi. Engineered: yes. Gtp-binding protein ypt1. Chain: y. Fragment: ypt1. Synonym: protein yp2. Engineered: yes.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: gdi1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: ypt1.

Biol. unit:

Dimer (from PQS)

Resolution:

1.48Å R-factor: 0.165 R-free: 0.193

Authors:

O.Pylypenko,A.Rak,K.Alexandrov

Key ref:

O.Pylypenko et al. (2006). Structure of doubly prenylated Ypt1:GDI complex and the mechanism of GDI-mediated Rab recycling. EMBO J, 25, 13-23. PubMed id: 16395334 DOI: 10.1038/sj.emboj.7600921

Date:

19-Oct-05 Release date: 17-Jan-06

Protein chain

P39958  (GDI1_YEAST) -  Rab GDP-dissociation inhibitor from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 451 a.a.

Struc: 442 a.a.

Protein chain

P01123  (YPT1_YEAST) -  GTP-binding protein YPT1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 206 a.a.

Struc: 194 a.a.

Enzyme reactions

• Enzyme class: Chains G, Y: E.C.?

DOI no: 10.1038/sj.emboj.7600921

EMBO J 25:13-23 (2006)

PubMed id: 16395334

Structure of doubly prenylated Ypt1:GDI complex and the mechanism of GDI-mediated Rab recycling.

O.Pylypenko, A.Rak, T.Durek, S.Kushnir, B.E.Dursina, N.H.Thomae, A.T.Constantinescu, L.Brunsveld, A.Watzke, H.Waldmann, R.S.Goody, K.Alexandrov.

ABSTRACT

In eukaryotic cells Rab/Ypt GTPases represent a family of key membrane traffic controllers that associate with their targeted membranes via C-terminally conjugated geranylgeranyl groups. GDP dissociation inhibitor (GDI) is a general and essential regulator of Rab recycling that extracts prenylated Rab proteins from membranes at the end of their cycle of activity and facilitates their delivery to the donor membranes. Here, we present the structure of a complex between GDI and a doubly prenylated Rab protein. We show that one geranylgeranyl residue is deeply buried in a hydrophobic pocket formed by domain II of GDI, whereas the other lipid is more exposed to solvent and is skewed across several atoms of the first moiety. Based on structural information and biophysical measurements, we propose mechanistic and thermodynamic models for GDI and Rab escort protein-mediated interaction of RabGTPase with intracellular membranes.

Selected figure(s)

Figure 1.
Figure 1 Structure of the doubly prenylated Ypt1:GDI complex. (A) Ribbon representation of GDI (blue) bound to Ypt1 (yellow). Domain I (dark blue), domain II (light blue), the Rab-binding platform (red), the C-terminus-binding region (CBR gold) and the mobile effector loop (MEL green) of GDI are highlighted. The Switch I and II regions of Ypt1 are highlighted in green and grey, respectively. The helices composing domain II of GDI are marked by letters. The isoprenoid moieties 1 (red) and 2 (dark yellow) are displayed in ball-and-stick representation. The GDP (atomic colours) and Mg2+ (magenta) ion are shown in the nucleotide-binding pocket in ball-and-stick and space filling representations, respectively. Unless otherwise indicated, this and other figures were prepared using ICM (Molsoft LLC). (B) Plot of a sigma A-weighted F[o]-F[c] map contoured at 2 (red) or at 0.6 (black) in the region of the geranylgeranyl. The maps were generated after several refinement rounds omitting the GG groups. The picture was generated with BobScript and RASTER3D (Merritt and Murphy, 1994; Esnouf, 1997). (C) Domain II of GDI from Ypt1GG:GDI complex displayed in ribbon representation (grey); the secondary structure elements are denoted as in (A). The last visible residues of the Ypt1 C-terminus and of the MEL of GDI are coloured blue and green, respectively. The geranylgeranyl moieties 1 (red) and 2 (blue) filling the lipid binding site are displayed in ball-and-stick representation.

Figure 3.
Figure 3 Model for the GDI-mediated Rab/Ypt interaction with the putative Rab receptors and membranes. (A) GDI-mediated delivery of prenylated RabGTPases to the membrane is proposed to involve docking of the Rab:GDI complex with a putative membrane Rab recruitment/GDF via a protein:protein interaction (2). The docked complex undergoes a conformational change, which leads to the transfer of the first and then the second geranylgeranyl moiety into the membrane and subsequently to the release of the Rab C-terminus from the CBR (3 and 4). Finally, GDI is released into the cytosol and the Rab protein enters its functional cycle. (B) GDI-mediated extraction of prenylated RabGTPases from the membrane. Initial recognition is mediated by the low-affinity interaction of the Rab-binding platform with the CBR of GDI (7). This leads to the positioning of GDI domain II on the lipid bilayer over the buried geranylgeranyl moieties of the Rab protein (8). The geranylgeranyl lipids are transferred from the membrane to the lipid binding sites on GDI in two consecutive steps (9 and 10), leading to dissociation of the complex from membrane (11).

The above figures are reprinted by permission from Macmillan Publishers Ltd: EMBO J (2006, 25, 13-23) copyright 2006.

Figures were selected by an automated process.