7EH2

Thermus thermophilus transcription initiation complex containing a template-strand pyrimidine at position TSS-2 and GpG RNA primer

7EH2 の概要

• エントリーDOI: 10.2210/pdb7eh2/pdb
• 分子名称: DNA-directed RNA polymerase subunit alpha, MAGNESIUM ION, DNA-directed RNA polymerase subunit beta, ... (11 entities in total)
• 機能のキーワード: thermus thermophilus, rna polymerase, transcription initiation, gpg, transcription, transcription-dna-rna complex, transcription/dna/rna
• 由来する生物種: Thermus thermophilus HB8; 詳細
• タンパク質・核酸の鎖数: 18
• 化学式量合計: 887729.74

構造登録者

Li, L.,Zhang, Y. (登録日: 2021-03-27, 公開日: 2021-07-14, 最終更新日: 2023-11-29)

主引用文献

Skalenko, K.S.,Li, L.,Zhang, Y.,Vvedenskaya, I.O.,Winkelman, J.T.,Cope, A.L.,Taylor, D.M.,Shah, P.,Ebright, R.H.,Kinney, J.B.,Zhang, Y.,Nickels, B.E.
Promoter-sequence determinants and structural basis of primer-dependent transcription initiation in Escherichia coli .
Proc.Natl.Acad.Sci.USA, 118:-, 2021

PubMed Abstract: Chemical modifications of RNA 5'-ends enable "epitranscriptomic" regulation, influencing multiple aspects of RNA fate. In transcription initiation, a large inventory of substrates compete with nucleoside triphosphates for use as initiating entities, providing an ab initio mechanism for altering the RNA 5'-end. In cells, RNAs with a 5'-end hydroxyl are generated by use of dinucleotide RNAs as primers for transcription initiation, "primer-dependent initiation." Here, we use massively systematic transcript end readout (MASTER) to detect and quantify RNA 5'-ends generated by primer-dependent initiation for ∼4 (∼1,000,000) promoter sequences in The results show primer-dependent initiation in involves any of the 16 possible dinucleotide primers and depends on promoter sequences in, upstream, and downstream of the primer binding site. The results yield a consensus sequence for primer-dependent initiation, YNNW, where TSS is the transcription start site, NN is the primer binding site, Y is pyrimidine, and W is A or T. Biochemical and structure-determination studies show that the base pair (nontemplate-strand base:template-strand base) immediately upstream of the primer binding site (Y:R, where R is purine) exerts its effect through the base on the DNA template strand (R) through interchain base stacking with the RNA primer. Results from analysis of a large set of natural, chromosomally encoded promoters support the conclusions from MASTER. Our findings provide a mechanistic and structural description of how TSS-region sequence hard-codes not only the TSS position but also the potential for epitranscriptomic regulation through primer-dependent transcription initiation.

PubMed: 34187896
DOI: 10.1073/pnas.2106388118

実験手法

X-RAY DIFFRACTION (3.34 Å)