6EI8

Crystal structure of human tRNA-dihydrouridine (20) synthase dsRBD F359A mutant

6EI8 の概要

• エントリーDOI: 10.2210/pdb6ei8/pdb
• 分子名称: tRNA-dihydrouridine(20) synthase [NAD(P)+]-like, SULFATE ION (3 entities in total)
• 機能のキーワード: double-stranded rna-binding domain, rna binding protein
• 由来する生物種: Homo sapiens (Human)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 13940.79

構造登録者

Bou-Nader, C.,Pecqueur, L.,Hamdane, D. (登録日: 2017-09-18, 公開日: 2018-10-10, 最終更新日: 2024-01-17)

主引用文献

Bou-Nader, C.,Pecqueur, L.,Barraud, P.,Fontecave, M.,Tisne, C.,Sacquin-Mora, S.,Hamdane, D.
Conformational Stability Adaptation of a Double-Stranded RNA-Binding Domain to Transfer RNA Ligand.
Biochemistry, 58:2463-2473, 2019

PubMed Abstract: The double-stranded RNA-binding domain (dsRBD) is a broadly distributed domain among RNA-maturing enzymes. Although this domain recognizes dsRNA's structures via a conserved canonical structure adopting an α-βββ-α topology, several dsRBDs can accommodate discrete structural extensions expanding further their functional repertoire. How these structural elements engage cooperative communications with the canonical structure and how they contribute to the dsRBD's overall folding are poorly understood. Here, we addressed these issues using the dsRBD of human dihydrouridine synthase-2 (hDus2) (hDus2-dsRBD) as a model. This dsRBD harbors N- and C-terminal extensions, the former being directly involved in the recognition of tRNA substrate of hDus2. These extensions engage residues that form a long-range hydrophobic network (LHN) outside the RNA-binding interface. We show by coarse-grain Brownian dynamics that the Nt-extension and its residues F359 and Y364 rigidify the major folding nucleus of the canonical structure via an indirect effect. hDus2-dsRBD unfolds following a two-state cooperative model, whereas both F359A and Y364A mutants, designed to destabilize this LHN, unfold irreversibly. Structural and computational analyses show that these mutants are unstable due to an increase in the dynamics of the two extensions favoring solvent exposure of α2-helix and weakening the main folding nucleus rigidity. This LHN appears essential for maintaining a thermodynamic stability of the overall system and eventually a functional conformation for tRNA recognition. Altogether, our findings suggest that functional adaptability of extended dsRBDs is promoted by a cooperative hydrophobic coupling between the extensions acting as effectors and the folding nucleus of the canonical structure.

PubMed: 31045345
DOI: 10.1021/acs.biochem.9b00111

実験手法

X-RAY DIFFRACTION (2.25 Å)