Structures of the human Pals1 PDZ domain with and without ligand suggest gated access of Crb to the PDZ peptide-binding groove

Ivanova, M.E.; Fletcher, G.C.; O'Reilly, N.; Purkiss, A.G.; Thompson, B.J.; McDonald, N.Q.

doi:10.1107/S139900471402776X

Figure 3
Comparison of ligand-free Pals1^PDZ and the Crb¹⁷–Pals1^PDZ complex. (a, b) Cartoon schematics of (a) ligand-free Pals1^PDZ and (b) the Crb¹⁷–Pals1^PDZ complex. (c) Superimposition of ligand-free Pals1^PDZ and the Crb¹⁷–Pals1^PDZ complex. Pals1^PDZ is shown in grey; Pals1 Phe318 and the carboxylate-binding loop are shown in red and the Crb¹⁷ peptide is shown in green. Elements with different conformers are highlighted in pink for unliganded Pals1^PDZ and in purple for the Crb¹⁷–Pals1^PDZ complex. (d) Close-up of the binding pocket of Pals1^PDZ (light grey) in the absence of peptide. The key structural elements which change conformation upon binding PBM are highlighted in pink. A glycerol molecule (shown in blue) occupies the PBM pocket, closely mimicking the carboxylate position of Crb¹⁷. (e) Sequence alignment of Pals1 isoforms across vertebrates and invertebrates. Conserved residues are highlighted in purple; darker purple indicates the most conserved residues. Residue numberings and secondary structures for human Pals1 are shown above and below the alignment, respectively; arrows represent β-strands and helices represent α-helices. Pals1 Phe318 and the carboxylate-binding loop are highlighted with red boxes and residues making contacts with the Crb¹⁷ peptide are highlighted in red. (f) Representative binding curves for a fluorescein-labelled Crb¹⁷ peptide binding to wild-type Pals1^PDZ (shown in green), Pals1^PDZ F318A mutant (shown in red) and Pals1^PDZ F318C mutant (shown in blue) measured by fluorescence polarization.

BIOLOGICAL
CRYSTALLOGRAPHY

ISSN: 1399-0047

Volume 71| Part 3| February 2015| Pages 555-564

doi:10.1107/S139900471402776X

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