Structure of RNA 3'-phosphate cyclase bound to substrate RNA

RNA. 2014 Oct;20(10):1560-6. doi: 10.1261/rna.045823.114. Epub 2014 Aug 26.


RNA 3'-phosphate cyclase (RtcA) catalyzes the ATP-dependent cyclization of a 3'-phosphate to form a 2',3'-cyclic phosphate at RNA termini. Cyclization proceeds through RtcA-AMP and RNA(3')pp(5')A covalent intermediates, which are analogous to intermediates formed during catalysis by the tRNA ligase RtcB. Here we present a crystal structure of Pyrococcus horikoshii RtcA in complex with a 3'-phosphate terminated RNA and adenosine in the AMP-binding pocket. Our data reveal that RtcA recognizes substrate RNA by ensuring that the terminal 3'-phosphate makes a large contribution to RNA binding. Furthermore, the RNA 3'-phosphate is poised for in-line attack on the P-N bond that links the phosphorous atom of AMP to N(ε) of His307. Thus, we provide the first insights into RNA 3'-phosphate termini recognition and the mechanism of 3'-phosphate activation by an Rtc enzyme.

Keywords: 2′,3′-cyclic phosphate termini; RNA 3′-phosphate termini; RtcA.

Publication types

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

MeSH terms

  • Adenosine Monophosphate / metabolism
  • Catalysis
  • Crystallography, X-Ray
  • Ligases / chemistry*
  • Ligases / genetics
  • Ligases / metabolism*
  • Models, Molecular
  • Mutagenesis, Site-Directed
  • Mutation / genetics
  • Protein Binding
  • Protein Conformation
  • Pyrococcus horikoshii / enzymology*
  • RNA / chemistry
  • RNA / genetics
  • RNA / metabolism*


  • Adenosine Monophosphate
  • RNA
  • Ligases
  • RNA 3'-terminal phosphate cyclase

Associated data

  • PDB/4O89
  • PDB/4O8J