PDBsum entry 2df6

Signaling protein

PDB id: 2df6

Contents

Protein chains

59 a.a. *

18 a.a. *

12 a.a. *

Waters ×141

* Residue conservation analysis

PDB id:

2df6

Name:

Signaling protein

Title:

Crystal structure of the sh3 domain of betapix in complex with a high affinity peptide from pak2

Structure:

Rho guanine nucleotide exchange factor 7. Chain: a, b. Fragment: sh3 domain(residues 10-63). Synonym: pak-interacting exchange factor beta, beta-pix. Engineered: yes. 18-mer from pak2. Chain: c, d. Fragment: residues 180-197. Engineered: yes

Source:

Rattus norvegicus. Norway rat. Organism_taxid: 10116. Gene: arhgef7, pak3bp, pixb. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Synthetic: yes. Other_details: the peptide was chemically synthesized. The sequence of the peptide is naturally found in human, rat.

Biol. unit:

Dimer (from PQS)

Resolution:

1.30Å R-factor: 0.201 R-free: 0.215

Authors:

A.Hoelz

Key ref:

A.Hoelz et al. (2006). Crystal structure of the SH3 domain of betaPIX in complex with a high affinity peptide from PAK2. J Mol Biol, 358, 509-522. PubMed id: 16527308 DOI: 10.1016/j.jmb.2006.02.027

Date:

25-Feb-06 Release date: 11-Apr-06

Protein chains

O55043  (ARHG7_RAT) -  Rho guanine nucleotide exchange factor 7 from Rattus norvegicus

Seq: 646 a.a.

Struc: 59 a.a.*

Protein chain

Q64303  (PAK2_RAT) -  Serine/threonine-protein kinase PAK 2 from Rattus norvegicus

Seq: 524 a.a.

Struc: 18 a.a.*

Protein chain

Q64303  (PAK2_RAT) -  Serine/threonine-protein kinase PAK 2 from Rattus norvegicus

Seq: 524 a.a.

Struc: 12 a.a.*

* PDB and UniProt seqs differ at 7 residue positions (black crosses)

Enzyme reactions

• Enzyme class 2: Chains A, B: E.C.?
• Enzyme class 3: Chains C, D: E.C.2.7.11.1 - non-specific serine/threonine protein kinase.
• Reaction:
  1. L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H⁺
  2. L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jmb.2006.02.027

J Mol Biol 358:509-522 (2006)

PubMed id: 16527308

Crystal structure of the SH3 domain of betaPIX in complex with a high affinity peptide from PAK2.

A.Hoelz, J.M.Janz, S.D.Lawrie, B.Corwin, A.Lee, T.P.Sakmar.

ABSTRACT

The p21-activated kinases (PAKs) are important effector proteins of the small GTPases Cdc42 and Rac and control cytoskeletal rearrangements and cell proliferation. The direct interaction of PAKs with guanine nucleotide exchange factors from the PIX/Cool family, which is responsible for the localization of PAK kinases to focal complexes in the cell, is mediated by a 24-residue peptide segment in PAKs and an N-terminal src homology 3 (SH3) domain in PIX/Cool. The SH3-binding segment of PAK contains the atypical consensus-binding motif PxxxPR, which is required for unusually high affinity binding. In order to understand the structural basis for the high affinity and specificity of the PIX-PAK interaction, we solved crystal structures for the N-terminal SH3 domain of betaPIX and for the complex of the atypical binding segment of PAK2 with the N-terminal SH3 domain of betaPIX at 0.92 A and 1.3A resolution, respectively. The asymmetric unit of the crystal contains two SH3 domains and two peptide ligands. The bound peptide adopts a conformation that allows for intimate contacts with three grooves on the surface of the SH3 domain that lie between the n-Src and RT-loops. Most notably, the arginine residue of the PxxxPR motif forms a salt-bridge and is tightly coordinated by a number of residues in the SH3 domain. This arginine-specific interaction appears to be the key determinant for the high affinity binding of PAK peptides. Furthermore, C-terminal residues of the peptide engage in additional interactions with the surface of the RT-loop, which significantly increases binding specificity. Compared to a recent NMR structure of a similar complex, our crystal structure reveals an alternate binding mode. Finally, we compare our crystal structure with the recently published betaPIX/Cbl-b complex structure, and suggest the existence of a molecular switch.

Selected figure(s)

Figure 4.
Figure 4. The interface between the bPIX-SH3 domain and the PAK2-derived peptide. (a) Stereo view of the structure of the bPIX-SH3/PAK2 complex (red and yellow) which is superimposed on the structure of the bPIX-SH3 domain (gray). (b) The simulated-annealed 2F[o] -F[c] electron density map, sliced at 2.5 s, is shown for the PAK peptide (yellow stick representation). The C^a trace of the bPIX-SH3 domain is shown in red below the transparent van der Waals representation of the surface (gray). (c) Close-up view of the entire interface. PAK2 residues are labeled in yellow, and bPIX-SH3 domain residues are labeled in red. Residues in PAK2 that are essential for the interaction are labeled in orange.

Figure 6.
Figure 6. Comparison of the bPIX-SH3/PAK2 structure to other bPIX-SH3 structures. (a) Superposition of the crystal and NMR structures of the bPIX-SH3/PAK complex. Peptides are illustrated in stick representation. The bPIX-SH3 surface is shown in gray, and the peptides are colored according to the legend in (a). (b) Structure of the bPIX-SH3/Cbl-b complex shown in ribbon representation (PDB code 2AK5). The two bPIX-SH3 domains and the Cbl-b peptide are colored according to the legend in (b). (c) Superposition of the bPIX-SH3/PAK2 crystal structure with the bPIX-SH3 B/Cbl-b crystal structure. bPIX-SH3 A has been removed for clarity. Peptides are illustrated in stick representation. The peptides of the crystal structures are colored according to the legend in (c).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 358, 509-522) copyright 2006.

Figures were selected by the author.