PDBsum entry 6dcc

Transferase/RNA

PDB id: 6dcc

Contents

Protein chain

221 a.a.

DNA/RNA

Ligands

SAH

SO4

Waters ×91

PDB id:

6dcc

Name:

Transferase/RNA

Title:

Structure of methylphosphate capping enzyme methyltransferase domain in complex with 5' end of 7sk RNA

Structure:

7sk snrna methylphosphate capping enzyme. Chain: a. Synonym: mepce,bicoid-interacting protein 3 homolog,bin3 homolog. Engineered: yes. Human 7sk RNA stem-loop 1 proximal methylated. Chain: b. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: mepce, bcdin3. Expressed in: escherichia coli. Expression_system_taxid: 469008. Synthetic: yes. Other_details: in vitro t7 polymerase transciption from synthetic DNA template, 5' methylated by cocrytallization with mepce and sam.

Resolution:

2.10Å R-factor: 0.177 R-free: 0.199

Authors:

Y.Yang,C.Eichhorn,D.Cascio,J.Feigon

Key ref:

Y.Yang et al. (2019). Structural basis of 7SK RNA 5'-γ-phosphate methylation and retention by MePCE. Nat Chem Biol, 15, 132-140. PubMed id: 30559425 DOI: 10.1038/s41589-018-0188-z

Date:

04-May-18 Release date: 19-Dec-18

Protein chain

Q7L2J0  (MEPCE_HUMAN) -  7SK snRNA methylphosphate capping enzyme from Homo sapiens

Seq: 689 a.a.

Struc: 221 a.a.

DNA/RNA chain

G5J-G-A-U-G-U-G-A-G-G-C-U-U-C-G-G-C-C-U-C-A-C-C-G-C-U-C-C-A-U-G-U-G-C-G-A 36 bases

Enzyme reactions

• Enzyme class: E.C.2.1.1.- - ?????

DOI no: 10.1038/s41589-018-0188-z

Nat Chem Biol 15:132-140 (2019)

PubMed id: 30559425

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

Y.Yang, C.D.Eichhorn, Y.Wang, D.Cascio, J.Feigon.

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.