Supplemental Figure 1C
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Fig. S1. Molecular modeling of the TRAF6 polyPro loop. (A) The
X-ray crystal structure coordinates for the TRAF2 MATH domain plus coiled-coil
region trimer bound to a TNFR2 peptide (Park et al., 1999) were examined using
RasMol software. Each of the three monomers is displayed as distinctly colored
backbone sticks overlaid with a red dot pattern representing the van der Waals
surfaces of individual atoms. Atoms involved in inter-subunit associations are
colored as solid spheres according to the backbone scheme for each subunit.
Proline 459 (P459) in TRAF2 is homologous to the conserved proline 462 (P462)
in TRAF6 (Park et al., 1999) and is colored red as a buried residue near each
interface. This proline is positioned immediately adjacent to arginine 458
(R458) in the same subunit. In turn, R458 is involved in an inter-domain ion
pair with aspartate 487 (D487) in the adjacent subunit that probably
contributes to MATH-domain multimerization. The immediate proximity of P459 to
R458 suggests that substitution of proline by alanine could result in a
perturbation of the backbone geometry, altering the alignment of the
inter-subunit ion pair. (B) The X-ray crystal structure coordinates for the
TRAF6 MATH monomer bound to a CD40 TRAF-binding peptide (Ye et al., 2002) is
orientationally aligned with the coordinates for the TRAF2 MATH domain plus
coiled-coil region trimer bound to the TNFR2-binding peptide (Park et al.,
1999). The alignment was accomplished by superimposition of the MATH domain
peptide backbones. The upper panel compares the two MATH domains in a
C-terminal view down the coiled-coil axis of the TRAF2 trimer. The TRAF6 MATH
domain and one similarly aligned MATH domain from TRAF2 are displayed as
space-filling models, whereas the remainder of TRAF2 is displayed as single
strands representing the course of the peptide backbones. The CD40 and TNFR2
peptides are indicated as red peptide backbones. The view for the lower panel
is a 90° x-axis rotation with respect to that shown in the upper panel. (C)
Comparison of the TRAF6 and TRAF2 MATH domains in the same orientation as in
the lower panel of B. The CD40 and TNFR2 peptides are purple and the backbone
structure of the TRAF6 polyPro loop, and the corresponding region of TRAF2, is
shown in red. Note that P459 in TRAF6 is not visible in TRAF6, since it is
buried within the structure. These models reveal that P459 in TRAF2, a
conserved proline found in all TRAF-family members (Park et al., 1999), is
buried within the MATH domain in an inaccessible location that might influence
the geometry of an ion pair that could be important for MATH-domain
inter-subunit association. The models also reveal that the two non-conserved
proline residues found only in TRAF6 are exposed on the outside surface within
the polyPro loop, where they could be available for interaction with the SH3
domain of Src.
