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Nat Struct Mol Biol. 2016 Oct;23(10):941-948. doi: 10.1038/nsmb.3282. Epub 2016 Aug 29.

Methyl transfer by substrate signaling from a knotted protein fold.

Author information

1
Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.
2
Center of New Technologies, University of Warsaw, Warsaw, Poland.
3
Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland.
4
RIKEN Systems and Structural Biology Center, Yokohama, Japan.
5
Graduate School of Science, University of Tokyo, Tokyo, Japan.
6
RIKEN Center for Life Science Technologies, Yokohama, Japan.
7
Department of Chemistry, Wesleyan University, Middletown, Connecticut, USA.
8
RIKEN Structural Biology Laboratory, Yokohama, Japan.
9
Department of Chemistry, University of Warsaw, Warsaw, Poland.

Abstract

Proteins with knotted configurations, in comparison with unknotted proteins, are restricted in conformational space. Little is known regarding whether knotted proteins have sufficient dynamics to communicate between spatially separated substrate-binding sites. TrmD is a bacterial methyltransferase that uses a knotted protein fold to catalyze methyl transfer from S-adenosyl methionine (AdoMet) to G37-tRNA. The product, m1G37-tRNA, is essential for life and maintains protein-synthesis reading frames. Using an integrated approach of structural, kinetic, and computational analysis, we show that the structurally constrained TrmD knot is required for its catalytic activity. Unexpectedly, the TrmD knot undergoes complex internal movements that respond to AdoMet binding and signaling. Most of the signaling propagates the free energy of AdoMet binding, thereby stabilizing tRNA binding and allowing assembly of the active site. This work demonstrates new principles of knots as organized structures that capture the free energies of substrate binding and facilitate catalysis.

PMID:
27571175
PMCID:
PMC5429141
DOI:
10.1038/nsmb.3282
[Indexed for MEDLINE]
Free PMC Article

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