8TG0

Solution NMR structure of the cold shock domain of the Arabidopsis thaliana glycine-rich protein AtGRP2

Summary for 8TG0

• Entry DOI: 10.2210/pdb8tg0/pdb
• NMR Information: BMRB: 51870
• Descriptor: Cold shock protein 2 (1 entity in total)
• Functional Keywords: glycine-rich protein, cold shock, rna binding protein
• Biological source: Arabidopsis thaliana (thale cress)
• Total number of polymer chains: 1
• Total formula weight: 9665.30

Authors

Pougy, K.C.,Almeida, F.C.L.,Pinheiro, A.S. (deposition date: 2023-07-12, release date: 2024-10-30, Last modification date: 2024-11-27)

Primary citation

Pougy, K.C.,Moraes, B.S.,Malizia-Motta, C.L.F.,Lima, L.M.T.R.,Sachetto-Martins, G.,Almeida, F.C.L.,Pinheiro, A.S.
Structural basis of nucleic acid recognition by the N-terminal cold shock domain of the plant glycine-rich protein AtGRP2.
J.Biol.Chem., 300:107903-107903, 2024

PubMed Abstract: AtGRP2 is a glycine-rich, RNA-binding protein that plays pivotal roles in abiotic stress response and flowering time regulation in Arabidopsis thaliana. AtGRP2 consists of an N-terminal cold shock domain (CSD) and two C-terminal CCHC-type zinc knuckles interspersed with glycine-rich regions. Here, we investigated the structure, dynamics, and nucleic acid binding properties of AtGRP2-CSD. The 2D [H,N] HSQC spectrum of AtGRP2-CSD revealed the presence of a partially folded intermediate in equilibrium with the folded state. The addition of eleven residues at the C-terminus stabilized the folded conformation. The three-dimensional structure of AtGRP2-CSD unveiled a β-barrel composed of five antiparallel β-strands and a 3 helical turn, along with an ordered C-terminal extension, a conserved feature in eukaryotic CSDs. Direct contacts between the C-terminal extension and the β3-β4 loop further stabilized the CSD fold. AtGRP2-CSD exhibited nucleic acid binding via solvent-exposed residues on strands β2 and β3, as well as the β3-β4 loop, with higher affinity for DNA over RNA, particularly favoring pyrimidine-rich sequences. Furthermore, DNA binding induced rigidity in the β3-β4 loop, evidenced by N-{H} NOE values. Mutation of residues W17, F26, and F37, in the central β-sheet, completely abolished DNA binding, highlighting the significance of π-stacking interactions in the binding mechanism. These results shed light on the mechanism of nucleic acid recognition employed by AtGRP2, creating a framework for the development of biotechnological strategies aimed at enhancing plant resistance to abiotic stresses.

PubMed: 39426727
DOI: 10.1016/j.jbc.2024.107903

Experimental method

SOLUTION NMR