Structural basis of 7SK RNA 5'-γ-phosphate methylation and retention by MePCE

Nat Chem Biol. 2019 Feb;15(2):132-140. doi: 10.1038/s41589-018-0188-z. Epub 2018 Dec 17.

Abstract

Among RNA 5'-cap structures, γ-phosphate monomethylation is unique to a small subset of noncoding RNAs, 7SK and U6 in humans. 7SK is capped by methylphosphate capping enzyme (MePCE), which has a second nonenzymatic role as a core component of the 7SK ribonuclear protein (RNP), an essential regulator of RNA transcription. We report 2.0- and 2.1-Å X-ray crystal structures of the human MePCE methyltransferase domain bound to S-adenosylhomocysteine (SAH) and uncapped or capped 7SK substrates, respectively. 7SK recognition is achieved by protein contacts to a 5'-hairpin-single-stranded RNA region, thus explaining MePCE's specificity for 7SK and U6. The structures reveal SAH and product RNA in a near-transition-state geometry. Unexpectedly, binding experiments showed that MePCE has higher affinity for capped versus uncapped 7SK, and kinetic data support a model of slow product release. This work reveals the molecular mechanism of methyl transfer and 7SK retention by MePCE for subsequent assembly of 7SK RNP.

Publication types

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

MeSH terms

  • HeLa Cells
  • Humans
  • Methylation
  • Methyltransferases / metabolism*
  • Methyltransferases / ultrastructure*
  • Organophosphates / metabolism
  • Phosphates
  • RNA Caps
  • RNA, Long Noncoding / metabolism
  • RNA, Small Nuclear / metabolism
  • RNA, Untranslated
  • S-Adenosylhomocysteine / metabolism

Substances

  • Organophosphates
  • Phosphates
  • RNA Caps
  • RNA, Long Noncoding
  • RNA, Small Nuclear
  • RNA, Untranslated
  • U6 small nuclear RNA
  • long non-coding RNA 7SK, human
  • methylphosphate
  • S-Adenosylhomocysteine
  • 7SK methylphosphate capping enzyme, human
  • Methyltransferases