4Y31

Crystal structure of yellow lupine LlPR-10.1A protein in ligand-free form

Summary for 4Y31

• Entry DOI: 10.2210/pdb4y31/pdb
• Related: 1bv1 1fm4 1icx 1ifv 1xdf 2flh 2qim 3e85 3ie5 4a80 4a81 4a83 4a85 4a86 4a87 4a8u 4a8v 4gy9 4jhg 4jhh 4jhi 4n3e 4psb 4q0k 4ryv
• Descriptor: Protein LlR18A, ACETATE ION (3 entities in total)
• Functional Keywords: pr-10 fold, ligand binding, phytohormone binding protein, trans-zeatin, cytokinin, plant protein
• Biological source: Lupinus luteus (European yellow lupin)
• Total number of polymer chains: 1
• Total formula weight: 16807.97

Authors

Sliwiak, J.,Michalska, K.,Sikorski, M.M.,Jaskolski, M. (deposition date: 2015-02-10, release date: 2015-12-09, Last modification date: 2024-01-10)

Primary citation

Sliwiak, J.,Dolot, R.,Michalska, K.,Szpotkowski, K.,Bujacz, G.,Sikorski, M.,Jaskolski, M.
Crystallographic and CD probing of ligand-induced conformational changes in a plant PR-10 protein.
J.Struct.Biol., 193:55-66, 2016

PubMed Abstract: Plant pathogenesis-related class 10 (PR-10) proteins are a family of abundant proteins initially identified as elements of the plant defense system. The key structural feature suggesting PR-10 functionality is a huge hydrophobic cavity created in the protein interior by a scaffold composed of an extended β-sheet wrapped around a long and flexible C-terminal α-helix. Several crystallographic and NMR studies have shown that the cavity can accommodate a variety of small molecule ligands, including phytohormones. The article describes ∼1.3 Å resolution crystal structures of a Lupinus luteus PR-10 isoform LlPR-10.1A, in its free form and in complex with trans-zeatin, a naturally occurring plant hormone belonging to the cytokinin group. Moreover we present the structure of the same protein where the saturation with zeatin is not complete. This set of three crystal structures allows us to track the structural adaptation of the protein upon trans-zeatin docking, as well as the sequence of the ligand-binding events, step-by-step. In addition, titration of LlPR-10.1A with trans-zeatin monitored in solution by CD spectra, confirmed the pattern of structural adaptations deduced from the crystallographic studies. The ligand-biding mode shows no similarity to other zeatin complexes of PR-10 proteins. The present work, which describes the first atomic models of the same PR-10 protein with and without a physiological ligand, reveals that the conformation of LlPR-10.1A undergoes a significant structural rearrangement upon trans-zeatin binding.

PubMed: 26644353
DOI: 10.1016/j.jsb.2015.11.008

Experimental method

X-RAY DIFFRACTION (1.32 Å)