6DCB image
Entry Detail
PDB ID:
6DCB
Keywords:
Title:
Structure of methylphosphate capping enzyme methyltransferase domain in complex with 5' end of 7SK RNA
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2018-05-04
Release Date:
2018-12-19
Method Details:
Experimental Method:
Resolution:
2.00 Å
R-Value Free:
0.17
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
P 63
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:7SK snRNA methylphosphate capping enzyme
Chain IDs:B (auth: A)
Chain Length:309
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polyribonucleotide
Description:human 7SK RNA stem-loop 1 proximal
Chain IDs:A (auth: B)
Chain Length:36
Number of Molecules:1
Biological Source:Homo sapiens
Primary Citation
Structural basis of 7SK RNA 5'-gamma-phosphate methylation and retention by MePCE.
Nat. Chem. Biol. 15 132 140 (2019)
PMID: 30559425 DOI: 10.1038/s41589-018-0188-z

Abstact

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.

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