Figure 6

Structure of Peb1. (A) An overall view of the molecular structure. The first 100 residues are colored white, and the last 133 in greyblue, highlighting the two-domain structure of Peb1. The two pseudosymmetric domains fold into sandwiches of alternating alpha helices and beta strands. The N and C-termini are marked with spheres. The ligand binding site is situated at the domain interphase in the middle of the molecule, and a bound aspartate is shown as a stick model. Peb1 binds two zinc cations, which are indicated as grey spheres and marked with Zn1 and Zn2. Pentapeptide insertion sites in the TAR1 region are colored purple, and are situated in the first helix at the core of the N-terminal domain, Nα1. Pentapeptide insertion sites in the TAR2 region are colored yellow, and cover the end of the third beta-strand at the core of the second domain, and part of the following helix, Cβ3 and Cα3. The location of the long alanine substitutions in TAR1 and TAR2 are colored green. The two terminal helices of the protein are also marked, Zα1 and Zα2. In the indicated aspartate, carbons are colored green, oxygens red and nitrogens blue. The same color scheme is used in all atomic structure. (B) A detailed view of helix Nα1. The side chains of large hydrophobic residues of Nα1 are colored brown, and interactions with the surroundings are highlighted. (C) A close-up of area of the second cluster of disruptive substitutions at the center of the molecule, next to the the ligand-binding site. Residues of the long Ala substitution in this region are shown in green, except for three branched hydrophobic residues, V174, I178 and L179, that are drawn with thick brown lines. The neighboring residues are shown in atomic colors. Val174, Asp175, Ile178 pack tightly to each other to form the ligand-binding pocket along with Lys20, Ala65, Arg68, Ala82, Thr83, Phe84, Thr85, Arg90, Ala132, Thr133, Tyr157, Tyr199 from both domains.