4GY9

Crystal Structure of Medicago truncatula Nodulin 13 (MtN13) in complex with N6-isopentenyladenine (2iP)

Summary for 4GY9

• Entry DOI: 10.2210/pdb4gy9/pdb
• Related: 1icx 1ifv 1xdf 2flh 2qim 3ei5 3rws 3us7
• Descriptor: MtN13 protein, N-(3-METHYLBUT-2-EN-1-YL)-9H-PURIN-6-AMINE, SODIUM ION, ... (5 entities in total)
• Functional Keywords: pr-10 fold, nodulin, nodulation, legume plant-rhizobium symbiosis, cytokinin binding, plant protein
• Biological source: Medicago truncatula (Barrel medic)
• Total number of polymer chains: 1
• Total formula weight: 19216.25

Authors

Ruszkowski, M.,Sikorski, M.,Jaskolski, M. (deposition date: 2012-09-05, release date: 2013-09-04, Last modification date: 2023-09-13)

Primary citation

Ruszkowski, M.,Szpotkowski, K.,Sikorski, M.,Jaskolski, M.
The landscape of cytokinin binding by a plant nodulin.
Acta Crystallogr.,Sect.D, 69:2365-2380, 2013

PubMed Abstract: Nodulation is an extraordinary symbiotic interaction between leguminous plants and nitrogen-fixing bacteria (rhizobia) that assimilate atmospheric nitrogen (in root nodules) and convert it into compounds suitable for the plant host. A class of plant hormones called cytokinins are involved in the nodulation process. In the model legume Medicago truncatula, nodulin 13 (MtN13), which belongs to the pathogenesis-related proteins of class 10 (PR-10), is expressed in the outer cortex of the nodules. In general, PR-10 proteins are small and monomeric and have a characteristic fold with an internal hydrophobic cavity formed between a seven-stranded antiparallel β-sheet and a C-terminal α-helix. Previously, some PR-10 proteins not related to nodulation were found to bind cytokinins such as trans-zeatin. Here, four crystal structures of the MtN13 protein are reported in complexes with several cytokinins, namely trans-zeatin, N6-isopentenyladenine, kinetin and N6-benzyladenine. All four phytohormones are bound in the hydrophobic cavity in the same manner and have excellent definition in the electron-density maps. The binding of the cytokinins appears to be strong and specific and is reinforced by several hydrogen bonds. Although the binding stoichiometry is 1:1, the complex is actually dimeric, with a cytokinin molecule bound in each subunit. The ligand-binding site in each cavity is formed with the participation of a loop element from the other subunit, which plugs the only entrance to the cavity. Interestingly, a homodimer of MtN13 is also formed in solution, as confirmed by small-angle X-ray scattering (SAXS).

PubMed: 24311578
DOI: 10.1107/S0907444913021975

Experimental method

X-RAY DIFFRACTION (2.04 Å)