PDBsum entry 3fay

Membrane protein

PDB id: 3fay

Contents

Protein chain

379 a.a. *

Ligands

TRS

Waters ×147

* Residue conservation analysis

PDB id:

3fay

Name:

Membrane protein

Title:

Crystal structure of the gap-related domain of iqgap1

Structure:

Ras gtpase-activating-like protein iqgap1. Chain: a. Fragment: gap-related domain (grd). Synonym: p195. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: iqgap1, kiaa0051. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.20Å R-factor: 0.228 R-free: 0.258

Authors:

V.B.Kurella,J.M.Richard,C.L.Parke,H.Bellamy,D.K.Worthylake

Key ref:

V.B.Kurella et al. (2009). Crystal structure of the GTPase-activating protein-related domain from IQGAP1. J Biol Chem, 284, 14857-14865. PubMed id: 19321438 DOI: 10.1074/jbc.M808974200

Date:

18-Nov-08 Release date: 24-Mar-09

Protein chain

P46940  (IQGA1_HUMAN) -  Ras GTPase-activating-like protein IQGAP1 from Homo sapiens

Seq: 1657 a.a.

Struc: 379 a.a.*

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

DOI no: 10.1074/jbc.M808974200

J Biol Chem 284:14857-14865 (2009)

PubMed id: 19321438

Crystal structure of the GTPase-activating protein-related domain from IQGAP1.

V.B.Kurella, J.M.Richard, C.L.Parke, L.F.Lecour, H.D.Bellamy, D.K.Worthylake.

ABSTRACT

IQGAP1 is a 190-kDa molecular scaffold containing several domains required for interaction with numerous proteins. One domain is homologous to Ras GTPase-activating protein (GAP) domains. However, instead of accelerating hydrolysis of bound GTP on Ras IQGAP1, using its GAP-related domain (GRD) binds to Cdc42 and Rac1 and stabilizes their GTP-bound states. We report here the crystal structure of the isolated IQGAP1 GRD. Despite low sequence conservation, the overall structure of the GRD is very similar to the GAP domains from p120 RasGAP, neurofibromin, and SynGAP. However, instead of the catalytic "arginine finger" seen in functional Ras GAPs, the GRD has a conserved threonine residue. GRD residues 1099-1129 have no structural equivalent in RasGAP and are seen to form an extension at one end of the molecule. Because the sequence of these residues is highly conserved, this region likely confers a functionality particular to IQGAP family GRDs. We have used isothermal titration calorimetry to demonstrate that the isolated GRD binds to active Cdc42. Assuming a mode of interaction similar to that displayed in the Ras-RasGAP complex, we created an energy-minimized model of Cdc42.GTP bound to the GRD. Residues of the GRD that contact Cdc42 map to the surface of the GRD that displays the highest level of sequence conservation. The model indicates that steric clash between threonine 1046 with the phosphate-binding loop and other subtle changes would likely disrupt the proper geometry required for GTP hydrolysis.

Selected figure(s)

Figure 1.
Experimental electron density. Density-modified experimental phases and λ[1] amplitudes (all |F| > 0) were used to calculate this map in the resolution range of 25-2.4 Å. The map is contoured at 1.4 σ. In the lower right of the picture are Tyr^1193 and Arg^1194.

Figure 2.
The IQGAP1 GRD and GAP-334 have very similar tertiary structures. The GRD (left) and GAP-334 (Protein Data Bank code 1WER; right) were superimposed using combinatorial extension (29) to align the coordinates for this figure (root mean square deviation = 3.3 Å for 312 Cα atoms). The cartoon has been colored orange and yellow for the Ex domains of the GRD and GAP-334, respectively. The central domains are colored blue or light blue, and the 31-residue insertion characteristic of IQGAP GRDs is colored green.3[10] helices are shown in dark gray, and a five-residue π helix containing the ^1192YYR^1194 motif in the GRD is shown in dark blue. Thr^1046 of the GRD and Arg^789 of GAP-334 are shown as stick representations in magenta.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2009, 284, 14857-14865) copyright 2009.

Figures were selected by an automated process.