PDBsum entry 2ext

RNA binding protein

PDB id: 2ext

Contents

Protein chains

63 a.a.

Ligands

TRP ×3

Waters ×65

References listed in PDB file

Key reference

Title

Rounding up: engineering 12-Membered rings from the cyclic 11-Mer trap.

Authors

J.G.Heddle, T.Yokoyama, I.Yamashita, S.Y.Park, J.R.Tame.

Ref.

Structure, 2006, 14, 925-933. [DOI no: 10.1016/j.str.2006.03.013]

PubMed id

16698553

Abstract

The protein TRAP (trp RNA binding attenuation protein) forms a highly thermostable ring-shaped 11-mer. By linking in tandem two, three, or four DNA sequences encoding TRAP monomers, we have engineered new rings that consist of 12 TRAP subunits and bind 12 ligand molecules. The hydrogen bonding pattern and buried surface area within and between subunits are essentially identical between the 11-mer and 12-mer crystal structures. Why do the artificial proteins choose to make single 12-mer rings? The 12-mer rings are highly sterically strained by their peptide linkers and far from thermostable. That proteins choose to adopt a strained conformation of few subunits rather than an unstrained one with 11 subunits demonstrates the importance of entropic factors in controlling protein-protein interactions in general.

Figure 2.
Figure 2. Crystal Structures of TRAP3 and TRAP4 Rings Compared to Wild-Type TRAP
Structures are shown as molecular surface representations with each subunit or subunit equivalent uniquely colored. (A) TRAP3, (B) TRAP4, and (C) Wild-type B. stearothermophilus TRAP. The rings are shown both along the rotation of molecular axis and perpendicular to it.

Figure 8.
Figure 8. A Schematic Diagram Showing Possible Oligomeric Forms of TRAP3 Protein
Monomer equivalents are shown as blue blocks, and their N and C termini equivalents are marked as N and C respectively. The peptide linkers (Ala-Ala-Ala-Met) shown in red connect the C-terminal residue of one monomer to the N-terminal residue of the next. In wild-type TRAP, the N and C termini lie at opposite faces of the ring, with the N-terminal residue pointing into the cavity and the C-terminal residue lying on the outer surface of the ring. The distance between the last visible N- and C-terminal residues in the wild-type structure (Ser5 and Lys73 respectively) is 37.8 Å. In TRAP3 and TRAP4, peptide loops (not visible in the electron density) connect the monomer equivalents as shown. (A) In the 12-mer ring form observed in the crystal, the peptide linkers must cross from one face of the ring to the other, as shown by the red lines. (B) An unstrained, imaginary form of TRAP3 in which the peptide linkers lie parallel, so that their folded domains (shown as blue blocks) can associate into three TRAP 11-mer rings essentially identical to wild-type TRAP rings, giving the form shown in (C), the imaginary tube-like form of TRAP3.

The above figures are reprinted by permission from Cell Press: Structure (2006, 14, 925-933) copyright 2006.