5ZYO

Crystal Structure of domain-swapped Circular-Permuted YbeA (CP74) from Escherichia coli

5ZYO の概要

• エントリーDOI: 10.2210/pdb5zyo/pdb
• 分子名称: Ribosomal RNA large subunit methyltransferase H (2 entities in total)
• 機能のキーワード: methyltransferase, domain-swapping, knot, circular permutation., transferase
• 由来する生物種: Escherichia coli K-12; 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 70561.70

構造登録者

Ko, K.T.,Huang, K.F.,Lyu, P.C.,Hsu, S.T.D. (登録日: 2018-05-26, 公開日: 2019-05-29, 最終更新日: 2024-03-27)

主引用文献

Ko, K.T.,Hu, I.C.,Huang, K.F.,Lyu, P.C.,Hsu, S.D.
Untying a Knotted SPOUT RNA Methyltransferase by Circular Permutation Results in a Domain-Swapped Dimer.
Structure, 27:1224-1233.e4, 2019

PubMed Abstract: YbeA from E. coli is a trefoil-knotted SpoU-TrmD (SPOUT) RNA methyltransferase. While its knotted motif plays a key functional role, it is unclear how the knotted topology emerged from evolution. Here, we reverse-engineered an unknotted circular permutant (CP) of YbeA by introducing a new opening at the knotting loop. The resulting CP folded into an unexpected domain-swapped dimer. Untying the knotted loop abrogated its function, perturbed its folding stability and kinetics, and induced allosteric dynamic changes. We speculated that the knotted loop of YbeA is under tension to keep the cofactor in a high-energy configuration while keeping the threading C-terminal helix being knotted. Circular permutation released the mechanical strain thereby allowing the spring-loaded threading helix to flip, to relax, and to form a domain-swapped dimer. Being knotted may be the consequence of selection pressure for the unique structure-function relationship of the SPOUT superfamily that exists in all kingdoms of life.

PubMed: 31104814
DOI: 10.1016/j.str.2019.04.004

実験手法

X-RAY DIFFRACTION (1.75 Å)