A Closed Binding Pocket and Global Destabilization Modify the Binding Properties of an Alternatively Spliced Form of the Second PDZ Domain of PTP-BL

Abstract

PTP-BL is a large phosphatase that is implicated in cellular processes as diverse as cytokinesis, actin-cytoskeletal rearrangement, and apoptosis. Five PDZ domains mediate its cellular role by binding to the C termini of target proteins, forming multiprotein complexes. The second PDZ domain (PDZ2) binds to the C termini of the tumor suppressor protein APC and the LIM domain-containing protein RIL; however, in one splice variant, PDZ2as, a 5 residue insertion abrogates this binding. The insert causes distinct structural and dynamical changes in the alternatively spliced PDZ2: enlarging the L1 loop between beta2 and beta3, both lengthening and changing the orientation of the alpha2 helix, giving the base of the binding pocket less flexibility to accommodate ligands, and destabilizing the entire domain. These changes render the binding pocket incapable of binding C termini, possibly having implications in the functional role of PTP-BL.

Evaluation of Energetic and Dynamic Coupling Networks in a PDZ Domain Protein

“…10 Determination of rotational correlation times and 15 N-derived model free parameters PDZ domains (∼10 kDa) are expected to have rotational correlation times, τ m , ∼6-7 ns. [44][45][46] Consistent with these expectations, our previous backbone characterization of PDZ2 dynamics, 10 at a protein concentration of ∼2 mM, indicated a τ m of ∼7.0 ns free or bound to a peptide ligand. At ∼2 mM concentration, analysis of I20F and H71Y relaxation data yielded τ m values of 6.2 and 6.5 ns, respectively.…”

Sequence-specific 1H, 13C, and 15N backbone assignment of the 28 kDa PDZ2/PDZ3 tandem domain of the protein tyrosine phosphatase PTP-BL

“…Therefore, 45% of the Ca and 42% of the linker proton amide resonances could be assigned. The chemical Figure 2 shows the combined 1 H and 15 N NMR chemical shift differences between the isolated PDZ2 domain and the PDZ2 domain as part of the PDZ2/PDZ3 tandem construct plotted versus the amino acid sequence of PDZ2 (Walma et al 2002(Walma et al , 2004Kachel et al 2003). Only minor to medium chemical shift differences can be detected.…”

“…Fig. 2 Combined 1 H and 15 N NMR chemical shift differences between the isolated PDZ2 domain and PDZ2 as part of the PDZ2/ PDZ3 tandem domain plotted versus the amino acid sequence of PDZ2 (Walma et al 2002(Walma et al , 2004Kachel et al 2003 …”

“…In addition, PTP-BL contains five PDZ (PSD-95, Disc large, Zonula occludens) domains and a C-terminal protein tyrosine phosphatase domain (Erdmann 2003). Recently, the structures of PDZ2b of PTP-Bas and PDZ2 of PTP-BL have been solved (Kachel et al 2003;Walma et al 2004). PDZ domains share a globular fold, consisting of two a helices and 6 b strands, that form two anti parallel b sheets (Doyle et al 1996;Moiras Cabral et al 1996).…”

Sequence-specific 1H, 13C, and 15N assignment of the extended PDZ3 domain of the protein tyrosine phosphatase basophil-like PTP-BL

“…In addition, PTP-BL contains five PDZ (PSD-95, Discs large, Zonula occludens) domains as well as a carboxy terminal protein tyrosine phosphatase domain (Erdmann 2003). Hitherto, only the structures of PDZ2b of PTP-Bas and PDZ2 of PTP-BL have been solved but not the structure of the PDZ3 domain (Kachel et al 2003;Walma et al 2004). PDZ domains share a globular fold that consists of two a-helices and 6 b-strands, which form two anti parallel b-sheets (Doyle et al 1996;Morais Cabral et al 1996).…”