RNA ligase RtcB splices 3'-phosphate and 5'-OH ends via covalent RtcB-(histidinyl)-GMP and polynucleotide-(3')pp(5')G intermediates

Proc Natl Acad Sci U S A. 2012 Apr 17;109(16):6072-7. doi: 10.1073/pnas.1201207109. Epub 2012 Apr 2.


A cherished tenet of nucleic acid enzymology holds that synthesis of polynucleotide 3'-5' phosphodiesters proceeds via the attack of a 3'-OH on a high-energy 5' phosphoanhydride: either a nucleoside 5'-triphosphate in the case of RNA/DNA polymerases or an adenylylated intermediate A(5')pp(5')N--in the case of polynucleotide ligases. RtcB exemplifies a family of RNA ligases implicated in tRNA splicing and repair. Unlike classic ligases, RtcB seals broken RNAs with 3'-phosphate and 5'-OH ends. Here we show that RtcB executes a three-step ligation pathway entailing (i) reaction of His337 of the enzyme with GTP to form a covalent RtcB-(histidinyl-N)-GMP intermediate; (ii) transfer of guanylate to a polynucleotide 3'-phosphate to form a polynucleotide-(3')pp(5')G intermediate; and (iii) attack of a 5'-OH on the -N(3')pp(5')G end to form the splice junction. RtcB is structurally sui generis, and its chemical mechanism is unique. The wide distribution of RtcB proteins in bacteria, archaea, and metazoa raises the prospect of an alternative enzymology based on covalently activated 3' ends.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Amino Acyl-tRNA Synthetases / genetics
  • Amino Acyl-tRNA Synthetases / metabolism*
  • Base Sequence
  • Binding Sites
  • Electrophoresis, Polyacrylamide Gel
  • Escherichia coli / enzymology
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism*
  • Guanosine Monophosphate / metabolism*
  • Guanosine Triphosphate / metabolism*
  • Histidine / genetics
  • Histidine / metabolism
  • Kinetics
  • Molecular Sequence Data
  • Mutation
  • Phosphates / metabolism
  • Polynucleotides / metabolism*
  • RNA Ligase (ATP) / genetics
  • RNA Ligase (ATP) / metabolism
  • RNA, Bacterial / genetics
  • RNA, Bacterial / metabolism


  • Escherichia coli Proteins
  • Phosphates
  • Polynucleotides
  • RNA, Bacterial
  • Histidine
  • Guanosine Monophosphate
  • Guanosine Triphosphate
  • Amino Acyl-tRNA Synthetases
  • RtcB protein, E coli
  • RNA Ligase (ATP)