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. 2013 Mar 5;21(3):355-64.
doi: 10.1016/j.str.2013.01.001. Epub 2013 Jan 31.

Structural basis for autoinhibition of the guanine nucleotide exchange factor FARP2

Xiaojing He  1 , Yi-Chun Kuo, Tyler J Rosche, Xuewu Zhang
Affiliations

Structural basis for autoinhibition of the guanine nucleotide exchange factor FARP2

Xiaojing He et al. Structure. .

Abstract

FARP2 is a Dbl-family guanine nucleotide exchange factor (GEF) that contains a 4.1, ezrin, radixin and moesin (FERM) domain, a Dbl-homology (DH) domain and two pleckstrin homology (PH) domains. FARP2 activates Rac1 or Cdc42 in response to upstream signals, thereby regulating processes such as neuronal axon guidance and bone homeostasis. How the GEF activity of FARP2 is regulated remained poorly understood. We have determined the crystal structures of the catalytic DH domain and the DH-PH-PH domains of FARP2. The structures reveal an auto-inhibited conformation in which the GEF substrate-binding site is blocked collectively by the last helix in the DH domain and the two PH domains. This conformation is stabilized by multiple interactions among the domains and two well-structured inter-domain linkers. Our cell-based activity assays confirm the suppression of the FARP2 GEF activity by these auto-inhibitory elements.

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Figures

Figure 1
Figure 1. Structure of the DH domain of FARP2
(A) Overall structure of the DH domain. Helix α6C is colored in yellow. The side-chains of Leu730 and Leu733 and neighboring residues are shown in stick and dot representations. (B) Superimposition of the FARP2 DH domain with the intersectin/Cdc42 complex (PDB ID: 1KI1). The PH domain in intersectin is omitted for clarity. Helix α6C in FARP2 resembles the switch II helix (dark blue) of Cdc42. Leu730 and Leu733 occupy the same positions as Leu67 and Leu70 in Cdc42, respectively. Two substitutions (His690 and Gln727 in FARP2) in the substrate-binding surface of the DH domain are highlighted. (C) Comparison of the kinked Helices α6C in the DH domains of FARP2, FGD5 and SOS. (D) Sequence alignment of the DH domains of mouse FARP2, human FARP1 and human intersectin. The stars highlight the positions of Leu730 and Leu733 in FARP2. The triangles mark the two key substitutions in the substrate-binding site in FARP2 (His690 and Gln727). See also Figure S1.
Figure 2
Figure 2. Structure of the DH-PH-PH domains of FARP2
(A) Schematic of the domain structure of FARP2. (B) Overall structure of the DH-PH-PH domains. The color scheme is the same as in (A). Dashed lines represent disordered loops in the structure. (C) Comparison of the DH structures in the DH-PH-PH domains (DH: cyan; Helix α6C: yellow) and the isolated DH domain (gray). The structures are rotated horizontally in relation to (B) by ~90°. (D) Blocking of the substrate-binding site by Helix α6C, PH1, PH2 and the PH1-PH2 linker. Cdc42 (blue semi-transparent surface) is docked by superimposing the intersectin/Cdc42 complex structure (PDB ID: 1KI1) on to the FARP2 DH-PH-PH structure. Intersectin is omitted for clarity. See also Figure S2.
Figure 3
Figure 3. Structure of PH1 and its interactions with Helix α6C and the DH-PH1 linker
(A) Overall structure of PH1 (light brown) together with Helix α6C (yellow), the DH-PH1 linker (green) and the PH1-PH2 linker (blue). Positively charged residues in the potential PtdInsP(s) binding site are highlighted. The side-chain of Lys831 is not built due to lack of electron density. (B) Interactions among PH1, Helix α6C and the DH-PH1 linker. (C) Sequence alignment of mouse FARP2 and human FARP1, starting from the DH-PH1 linker and ending at the C-terminus of PH2. The structured linker regions are highlighted by boxes, colored as in (A). Secondary structural elements are assigned based on the DH-PH-PH structure of FARP2. See also Figure S3.
Figure 4
Figure 4. Structure of the PH1-PH2 linker and its interactions with PH1 and PH2
(A) Interactions made by the first helix in the PH1-PH2 linker. (B) Interactions made by the strand and the second helix in the PH1-PH2 linker.
Figure 5
Figure 5. Interface between PH2 and the DH domain
See also Figure S4.
Figure 6
Figure 6. Cell-based GEF activity assays for FARP2
(A) Assays of FARP2 activity towards Cdc42. Representative blots from five independent experiments are shown. Quantifications of the results are in the lower panel. The level of GTP-bound Cdc42 normalized by the total expression level from cells transfected with the control vector is arbitrarily set to 1. Levels of GTP-bound Cdc42 from cells expressing various FARP2 constructs are presented by fold increase (mean ± S.E. of the five experiments) over the control. FL, full-length FARP2; FLL730R/L733Q, full-length FARP2 with the L730R/L733Q mutations; ΔPH2, PH2-truncated FARP2; ΔPH2L730R/L733Q, PH2-truncated FARP2 with the L730R/L733Q mutations. Lower bands in the FLAG-FARP2 blots are likely degradation products of FARP2. (B) Assays of FARP2 activity towards Rac1. Data are presented as in (A). The p value was calculated from Student's t test. See also Figure S5.
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