7kee

From Proteopedia

RNA polymerase II elongation complex with unnatural base dTPT3, rNaMTP bound to E-site

Structural highlights

7kee is a 10 chain structure with sequence from Saccharomyces cerevisiae S288C and Synthetic construct. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 3.45Å
Ligands:	, , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

RPAB1_YEAST DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Common component of RNA polymerases I, II and III which synthesize ribosomal RNA precursors, mRNA precursors and many functional non-coding RNAs, and small RNAs, such as 5S rRNA and tRNAs, respectively. Pol II is the central component of the basal RNA polymerase II transcription machinery. Pols are composed of mobile elements that move relative to each other. In Pol II, RPB5 is part of the lower jaw surrounding the central large cleft and thought to grab the incoming DNA template. Seems to be the major component in this process (By similarity).

Publication Abstract from PubMed

The development of unnatural base pairs (UBPs) has greatly increased the information storage capacity of DNA, allowing for transcription of unnatural RNA by the heterologously expressed T7 RNA polymerase (RNAP) in Escherichia coli. However, little is known about how UBPs are transcribed by cellular RNA polymerases. Here, we investigated how synthetic unnatural nucleotides, NaM and TPT3, are recognized by eukaryotic RNA polymerase II (Pol II) and found that Pol II is able to selectively recognize UBPs with high fidelity when dTPT3 is in the template strand and rNaMTP acts as the nucleotide substrate. Our structural analysis and molecular dynamics simulation provide structural insights into transcriptional processing of UBPs in a stepwise manner. Intriguingly, we identified a novel 3'-RNA binding site after rNaM addition, termed the swing state. These results may pave the way for future studies in the design of transcription and translation strategies in higher organisms with expanded genetic codes.

Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II.,Oh J, Shin J, Unarta IC, Wang W, Feldman AW, Karadeema RJ, Xu L, Xu J, Chong J, Krishnamurthy R, Huang X, Romesberg FE, Wang D Nat Chem Biol. 2021 Aug;17(8):906-914. doi: 10.1038/s41589-021-00817-3. Epub 2021 , Jun 17. PMID:34140682^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Oh J, Shin J, Unarta IC, Wang W, Feldman AW, Karadeema RJ, Xu L, Xu J, Chong J, Krishnamurthy R, Huang X, Romesberg FE, Wang D. Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II. Nat Chem Biol. 2021 Aug;17(8):906-914. PMID:34140682 doi:10.1038/s41589-021-00817-3