Electrostatic Potential in the tRNA Binding Evolution of Dihydrouridine Synthases

Biochemistry. 2018 Sep 18;57(37):5407-5414. doi: 10.1021/acs.biochem.8b00584. Epub 2018 Aug 31.

Abstract

Dihydrouridine (D) is an abundant modified base of tRNA found in the majority of living organisms. This base is synthesized via an NADPH-dependent reduction of specific uridines by the dihydrouridine synthases (Dus), a large family of flavoenzymes comprising eight subfamilies. Almost all of these enzymes function with only two conserved domains, an N-terminal catalytic domain (TBD) adopting a TIM barrel fold and a unique C-terminal helical domain (HD) devoted to tRNA recognition, except for the animal U20-specific Dus2 enzyme. Curiously, this enzyme is distinguished from paralogues and its fungi orthologues by the acquisition of an additional domain, a double stranded RNA binding domain (dsRBD), which serves as the main tRNA binding module. On the basis of a homology model of yeast Dus2 and the crystallographic structure of a human Dus2 variant (TBD + HD) lacking dsRBD, we herein show that the HD surface of the human enzyme is less electropositive than that of its yeast orthologue. This is partly due to two positively charged residues, K304 and K315, present in yeast and more broadly in fungi Dus2 that are replaced by E294 and Q305 in human and conserved among animals Dus2. By artificially reintroducing these positive charges in human Dus2 lacking dsRBD, we restored a functional tRNA binding in this enzyme variant. Altogether, these results suggest that the electrostatic potential changes of HD have likely played a key role in the emergence of a new tRNA binding mode among Dus2 enzymes.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Catalytic Domain
  • Crystallography, X-Ray
  • Evolution, Molecular
  • Humans
  • NADPH Oxidases / metabolism
  • Oxidoreductases / chemistry
  • Oxidoreductases / genetics
  • Oxidoreductases / metabolism*
  • Protein Binding
  • Protein Conformation
  • RNA, Transfer / chemistry
  • RNA, Transfer / metabolism*
  • Saccharomyces cerevisiae / enzymology*
  • Saccharomyces cerevisiae Proteins / chemistry
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Static Electricity*
  • Substrate Specificity

Substances

  • Saccharomyces cerevisiae Proteins
  • RNA, Transfer
  • Oxidoreductases
  • SMM1 protein, S cerevisiae
  • tRNA dihydrouridine synthase-2, human
  • NADPH Oxidases