PDBsum entry 1fkm

Endocytosis/exocytosis

PDB id: 1fkm

Contents

Protein chain

322 a.a. *

Waters ×166

* Residue conservation analysis

PDB id:

1fkm

Name:

Endocytosis/exocytosis

Title:

Crystal structure of the ypt/rab-gap domain of gyp1p

Structure:

Protein (gyp1p). Chain: a. Fragment: ypt/rab-gap domain, residues 248-637. Synonym: orf yor070c. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Other_details: genomic DNA

Biol. unit:

Dimer (from PQS)

Resolution:

1.90Å R-factor: 0.199 R-free: 0.225

Authors:

A.Rak,R.Fedorov,K.Alexandrov,S.Albert,R.S.Goody,D.Gallwitz, A.J.Scheidig

Key ref:

A.Rak et al. (2000). Crystal structure of the GAP domain of Gyp1p: first insights into interaction with Ypt/Rab proteins. EMBO J, 19, 5105-5113. PubMed id: 11013213 DOI: 10.1093/emboj/19.19.5105

Date:

09-Aug-00 Release date: 09-Feb-01

Protein chain

Q08484  (GYP1_YEAST) -  GTPase-activating protein GYP1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 637 a.a.

Struc: 322 a.a.

DOI no: 10.1093/emboj/19.19.5105

EMBO J 19:5105-5113 (2000)

PubMed id: 11013213

Crystal structure of the GAP domain of Gyp1p: first insights into interaction with Ypt/Rab proteins.

A.Rak, R.Fedorov, K.Alexandrov, S.Albert, R.S.Goody, D.Gallwitz, A.J.Scheidig.

ABSTRACT

We present the 1.9 A resolution crystal structure of the catalytic domain of Gyp1p, a specific GTPase activating protein (GAP) for Ypt proteins, the yeast homologues of Rab proteins, which are involved in vesicular transport. Gyp1p is a member of a large family of eukaryotic proteins with shared sequence motifs. Previously, no structural information was available for any member of this class of proteins. The GAP domain of Gyp1p was found to be fully alpha-helical. However, the observed fold does not superimpose with other alpha-helical GAPs (e.g. Ras- and Cdc42/Rho-GAP). The conserved and catalytically crucial arginine residue, identified by mutational analysis, is in a comparable position to the arginine finger in the Ras- and Cdc42-GAPs, suggesting that Gyp1p utilizes an arginine finger in the GAP reaction, in analogy to Ras- and Cdc42-GAPs. A model for the interaction between Gyp1p and the Ypt protein satisfying biochemical data is given.

Selected figure(s)

Figure 4.
Figure 4 The putative Ypt binding cleft. (A) Electrostatic surface representations viewed into the concave side of the molecule. The figure was generated using the program GRASP (Nicholls et al., 1993) and rendered with the program raster3D (Merritt and Murphy, 1994). Red indicates negatively charged (-7 kT) and blue positively charged regions (+7 kT). (B) Surface CPK representation of the Gyp1p Ypt-GAP domain shown in the same orientation as in (A). Residues that are highly conserved in the different Gyp Ypt-GAP domains are coloured pink; well conserved residues are coloured yellow (see sequence alignment, Figure 2). Residues that are solvent accessible and form the surface of the cleft are labelled.

Figure 5.
Figure 5 Docking approach for the complex between Gyp1p and Ypt51p-GTP, modelled manually on the basis of known GAP–GTPase structures. (A) Active site of the complex formed between p120-GAP and H-Ras p21(GDP-AlF[3]). The hydrogen bonds between GAP residues Arg789 and Arg903 and H-Ras p21 residues Gln61 and Glu63 as well as with AlF[3] are indicated. This specific hydrogen bond network and the orientation of the side chains were used as a model for manual docking of Ypt51-GTP to Gyp1-46p. (B) Close-up view of the active site in the putative Gyp1-46p–Ypt51-GTP complex. For the interaction between the side chain of Arg343 and the -phosphate group, the salt bridge formed between Arg343 and Asp340 has to be broken. Gln66 of Ypt51p is well oriented to become positioned closer to the -phosphate by forming a hydrogen bond between its side chain and the main chain carbonyl group of Arg343 of Gyp1p. (C) Ribbon representation of the putative complex. The orientation of Gyp1-46p is the same as in Figure 1. The essential arginine Arg343 of Gyp1p, the active site glutamine Gln66 of Ypt51p and the bound nucleotide GTP are shown in ball-and-stick representation. This figure was generated using the programs BOBSCRIPT (Esnouf, 1997) and raster3D (Merritt and Murphy, 1994).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 5105-5113) copyright 2000.

Figures were selected by an automated process.