5ZYO

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

Summary for 5ZYO

• Entry DOI: 10.2210/pdb5zyo/pdb
• Descriptor: Ribosomal RNA large subunit methyltransferase H (2 entities in total)
• Functional Keywords: methyltransferase, domain-swapping, knot, circular permutation., transferase
• Biological source: Escherichia coli K-12; More
• Total number of polymer chains: 4
• Total formula weight: 70561.70

Authors

Ko, K.T.,Huang, K.F.,Lyu, P.C.,Hsu, S.T.D. (deposition date: 2018-05-26, release date: 2019-05-29, Last modification date: 2024-03-27)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.75 Å)