9C66

Structure of the Mena EVH1 domain bound to the polyproline segment of PTP1B

Summary for 9C66

• Entry DOI: 10.2210/pdb9c66/pdb
• Descriptor: Protein enabled homolog, poly-proline segment of PTP1B, 1,2-ETHANEDIOL, ... (5 entities in total)
• Functional Keywords: mena, structural protein
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 2
• Total formula weight: 14223.04

Authors

LaComb, L.,Fedorov, E.,Bonanno, J.B.,Almo, S.C.,Ghosh, A. (deposition date: 2024-06-07, release date: 2024-08-28, Last modification date: 2024-10-23)

Primary citation

LaComb, L.,Ghosh, A.,Bonanno, J.B.,Nilson, D.J.,Poppel, A.J.,Dada, L.,Cahill, S.M.,Maianti, J.P.,Kitamura, S.,Cowburn, D.,Almo, S.C.
Insights into the Interaction Landscape of the EVH1 Domain of Mena.
Biochemistry, 63:2183-2195, 2024

PubMed Abstract: The Enabled/VASP homology 1 (EVH1) domain is a small module that interacts with proline-rich stretches in its ligands and is found in various signaling and scaffolding proteins. Mena, the mammalian homologue of Ena, is involved in diverse actin-associated events, such as membrane dynamics, bacterial motility, and tumor intravasation and extravasation. Two-dimensional (2D) H-N HSQC NMR was used to study Mena EVH1 binding properties, defining the amino acids involved in ligand recognition for the physiological ligands ActA and PCARE, and a synthetic polyproline-inspired small molecule (hereafter inhibitor ). Chemical shift perturbations indicated that proline-rich segments bind in the conserved EVH1 hydrophobic cleft. The PCARE-derived peptide elicited more perturbations compared to the ActA-derived peptide, consistent with a previous report of a structural alteration in the solvent-exposed β7-β8 loop. Unexpectedly, EVH1 and the proline-rich segment of PTP1B did not exhibit NMR chemical shift perturbations; however, the high-resolution crystal structure implicated the conserved EVH1 hydrophobic cleft in ligand recognition. Intrinsic steady-state fluorescence and fluorescence polarization assays indicate that residues outside the proline-rich segment enhance the ligand affinity for EVH1 ( = 3-8 μM). Inhibitor displayed tighter binding ( ∼ 0.3 μM) and occupies the same EVH1 cleft as physiological ligands. These studies revealed that the EVH1 domain enhances ligand affinity through recognition of residues flanking the proline-rich segments. Additionally, a synthetic inhibitor binds more tightly to the EVH1 domain than natural ligands, occupying the same hydrophobic cleft.

PubMed: 39138154
DOI: 10.1021/acs.biochem.4c00331

Experimental method

X-RAY DIFFRACTION (1.4 Å)