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

Authors

Yuan Yang, UCLA
Catherine D. Eichhorn, UCLAFollow
Yaqiang Wang, UCLA
Duilio Cascio, UCLA
Juli Feigon, UCLAFollow

Date of this Version

2019

Citation

Nat Chem Biol. 2019 February ; 15(2): 132–140

Comments

HHS Public Access

doi:10.1038/s41589-018-0188-z

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 non-enzymatic role as a core component of the 7SK RNP that is an essential regulator of RNA transcription. We report 2.0 and 2.1 Å X-ray crystal structures of 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, explaining MePCE specificity for 7SK and U6. The structures reveal SAH and product RNA in a near-transition state geometry. Surprisingly, binding experiments show that MePCE has higher affinity for capped vs uncapped 7SK, with kinetic data supporting a slow product release model. This work reveals the molecular mechanism of methyl transfer and 7SK retention by MePCE for subsequent assembly of 7SK RNP.