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Untying a Knotted SPOUT RNA Methyltransferase by Circular Permutation Results in a Domain-Swapped Dimer

40 Pages Posted: 26 Feb 2019 Sneak Peek Status: Published

See all articles by Kuang-Ting Ko

Kuang-Ting Ko

Academia Sinica - Institute of Biological Chemistry; National Tsing Hua University - Institute of Bioinformatics and Structural Biology

I-Chen Hu

National Tsing Hua University - Institute of Bioinformatics and Structural Biology

Kai-Fa Huang

Academia Sinica - Institute of Biological Chemistry

Ping-Chiang Lyu

Academia Sinica - Institute of Biological Chemistry; National Tsing Hua University - Department of Medical Sciences

Shang-Te Danny Hsu

Academia Sinica - Institute of Biological Chemistry; National Taiwan University - Institute of Biochemical Sciences,

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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.

Suggested Citation

Ko, Kuang-Ting and Hu, I-Chen and Huang, Kai-Fa and Lyu, Ping-Chiang and Hsu, Shang-Te Danny, Untying a Knotted SPOUT RNA Methyltransferase by Circular Permutation Results in a Domain-Swapped Dimer (Januaary 16, 2019). Available at SSRN: https://ssrn.com/abstract=3316811 or http://dx.doi.org/10.2139/ssrn.3316811
This is a paper under consideration at Cell Press and has not been peer-reviewed.

Kuang-Ting Ko

Academia Sinica - Institute of Biological Chemistry

Taipei, 11529
Taiwan

National Tsing Hua University - Institute of Bioinformatics and Structural Biology

Hsinchu, 30013
Taiwan

I-Chen Hu

National Tsing Hua University - Institute of Bioinformatics and Structural Biology

Hsinchu, 30013
Taiwan

Kai-Fa Huang

Academia Sinica - Institute of Biological Chemistry

Taipei, 11529
Taiwan

Ping-Chiang Lyu

Academia Sinica - Institute of Biological Chemistry

Taipei, 11529
Taiwan

National Tsing Hua University - Department of Medical Sciences

Hsinchu, 30013
Taiwan

Shang-Te Danny Hsu (Contact Author)

Academia Sinica - Institute of Biological Chemistry ( email )

Taipei, 11529
Taiwan

National Taiwan University - Institute of Biochemical Sciences, ( email )

Taipei, 10617
Taiwan

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