title: Methyl transfer by substrate signaling from a knotted protein fold.
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.
authors: Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.
authors: Thomas
authors: T
authors: Christian
authors: Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.
authors: Reiko
authors: R
authors: Sakaguchi
authors: Center of New Technologies, University of Warsaw, Warsaw, Poland.|Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw, Warsaw, Poland.
authors: Agata P
authors: AP
authors: Perlinska
authors: Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.
authors: Georges
authors: G
authors: Lahoud
authors: RIKEN Systems and Structural Biology Center, Yokohama, Japan.|Graduate School of Science, University of Tokyo, Tokyo, Japan.|RIKEN Center for Life Science Technologies, Yokohama, Japan.
authors: Takuhiro
authors: T
authors: Ito
authors: Department of Chemistry, Wesleyan University, Middletown, Connecticut, USA.
authors: Erika A
authors: EA
authors: Taylor
authors: RIKEN Systems and Structural Biology Center, Yokohama, Japan.|Graduate School of Science, University of Tokyo, Tokyo, Japan.|RIKEN Structural Biology Laboratory, Yokohama, Japan.
authors: Shigeyuki
authors: S
authors: Yokoyama
authors: Center of New Technologies, University of Warsaw, Warsaw, Poland.|Department of Chemistry, University of Warsaw, Warsaw, Poland.
authors: Joanna I
authors: JI
authors: Sulkowska
authors: Department of Biochemistry and Molecular Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.
authors: Ya-Ming
authors: YM
authors: Hou
mesh_terms: D004926:Escherichia coli / Q000737:chemistry / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000378:metabolism*; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D017510:Protein Folding; D012343:RNA, Transfer / Q000737:chemistry / Q000378:metabolism*; D012436:S-Adenosylmethionine / Q000378:metabolism; D013379:Substrate Specificity; D012359:tRNA Methyltransferases / Q000737:chemistry / Q000378:metabolism*
chemical_list: D029968:Escherichia coli Proteins; D012436:S-Adenosylmethionine; D012343:RNA, Transfer; C489297:TrmD protein, E coli; D012359:tRNA Methyltransferases