PDBsum entry 2gnc

Signaling protein

PDB id: 2gnc

Contents

Protein chains

55 a.a. *

Waters ×171

* Residue conservation analysis

PDB id:

2gnc

Name:

Signaling protein

Title:

Crystal structure of srgap1 sh3 domain in the slit-robo signaling pathway

Structure:

Slit-robo rho gtpase-activating protein 1. Chain: a, b. Fragment: sh3 domain. Synonym: srgap1, rho-gtpase- activating protein 13, fragment. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.80Å R-factor: 0.208 R-free: 0.257

Authors:

X.Li,Y.Liu,F.Gao,M.Bartlam,J.Y.Wu,Z.Rao

Key ref:

X.Li et al. (2006). Structural basis of Robo proline-rich motif recognition by the srGAP1 Src homology 3 domain in the Slit-Robo signaling pathway. J Biol Chem, 281, 28430-28437. PubMed id: 16857672 DOI: 10.1074/jbc.M604135200

Date:

10-Apr-06 Release date: 18-Jul-06

Protein chains

Q91Z69  (SRGP1_MOUSE) -  SLIT-ROBO Rho GTPase-activating protein 1 from Mus musculus

Seq: 1062 a.a.

Struc: 55 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1074/jbc.M604135200

J Biol Chem 281:28430-28437 (2006)

PubMed id: 16857672

Structural basis of Robo proline-rich motif recognition by the srGAP1 Src homology 3 domain in the Slit-Robo signaling pathway.

X.Li, Y.Chen, Y.Liu, J.Gao, F.Gao, M.Bartlam, J.Y.Wu, Z.Rao.

ABSTRACT

The Slit-Robo (sr) GTPase-activating protein (GAPs) are important components in the intracellular pathway mediating Slit-Robo signaling in axon guidance and cell migration. We report the first crystal structure of the srGAP1 SH3 domain at 1.8-A resolution. The unusual side chain conformation of the conserved Phe-13 in the P1 pocket renders the ligand binding pocket shallow and narrow, which contributes toward the low binding affinity. Moreover, the opposing electrostatic charge and the hydrophobic properties of the P3 specificity pocket are consistent with the observed binding characteristics of the srGAP1 SH3 domain to its ligand. Surface plasmon resonance experiments indicate that the srGAP1 SH3 domain interacts with its natural ligand inaCtoN orientation. The srGAP1 SH3 domain can bind to both the CC2 and CC3 motifs in vitro. The N-terminal two acidic residues in the CC3 motif recognition site are necessary for srGAP1 SH3 domain binding. A longer CC3 peptide (CC3-FL) binds with greater affinity than its shorter counterpart, suggesting that the residues surrounding the proline-rich core are important for protein-peptide interactions. Our study reveals previously unknown properties of the srGAP-Robo interaction. Our data provide a structural basis for the srGAP-Robo interaction, consistent with the role of the Robo intracellular domain in interacting with other downstream signaling molecules and mediating versatile and dynamic responses to axon guidance and cell migration cues.

Selected figure(s)

Figure 3.
FIGURE 3. Stereo view showing a comparison of the srGAP1 SH3 domain with other SH3 domain structures. The residues forming the ligand binding pockets are shown in ball-and-stick representations. Molecule A of the srGAP1 SH3 domain is colored blue and molecule B is colored spring green, the -spectrin SH3 domain (PDB code 1BK2) (24) is colored gold, the Crk-N SH3 domain (PDB code 1CKA) (28) is colored brown, and the Abl tyrosine kinase SH3 domain (PDB code 1ABO) (29) is colored magenta. Residues are labeled corresponding to their positions in the srGAP1 SH3 domain.

Figure 5.
FIGURE 5. Surface representations of the SH3 domains from Crk-N complexed with C3G peptide, Abl complex with 3BP1, and srGAP1. The views on the left depict surface accessible hydrophobic regions colored in yellow. On the right are representations of electrostatic potential showing the peptide binding surface of the SH3 domains with the n-Src loops pointing toward the top, in which the positive electrostatic potential is colored in blue, negative electrostatic potential is colored in red, and hydrophobic surface is colored white. Peptides are in ball-and-stick representation. Coordinates for the SH3 domains of Crk-N and Abl were obtained from the Protein Data Bank. In the surface of the SH3 domain of srGAP1, the red circles indicate the four pockets in the ligand binding groove. The figure was produced by CCP4mg and PyMOL.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 28430-28437) copyright 2006.

Figures were selected by an automated process.