5ZYO image
Entry Detail
PDB ID:
5ZYO
Keywords:
Title:
Crystal Structure of domain-swapped Circular-Permuted YbeA (CP74) from Escherichia coli
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2018-05-26
Release Date:
2019-05-29
Method Details:
Experimental Method:
Resolution:
1.75 Å
R-Value Free:
0.19
R-Value Work:
0.16
R-Value Observed:
0.17
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Ribosomal RNA large subunit methyltransferase H
Chain IDs:A, B, C, D
Chain Length:158
Number of Molecules:4
Biological Source:Escherichia coli K-12
Primary Citation
Untying a Knotted SPOUT RNA Methyltransferase by Circular Permutation Results in a Domain-Swapped Dimer.
Structure 27 1224 1233.e4 (2019)
PMID: 31104814 DOI: 10.1016/j.str.2019.04.004

Abstact

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.

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