7EH1
Thermus thermophilus transcription initiation complex containing a template-strand purine at position TSS-2, GpG RNA primer, and CMPcPP
Summary for 7EH1
| Entry DOI | 10.2210/pdb7eh1/pdb |
| Descriptor | DNA-directed RNA polymerase subunit alpha, 1,4-BUTANEDIOL, ZINC ION, ... (13 entities in total) |
| Functional Keywords | thermus thermophilus, rna polymerase, transcription initiation, gpg, cmpcpp, transcription-dna-rna complex, transcription/dna/rna |
| Biological source | Thermus thermophilus HB8 More |
| Total number of polymer chains | 9 |
| Total formula weight | 444620.38 |
| Authors | |
| Primary citation | 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 Cited by 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: 34187896DOI: 10.1073/pnas.2106388118 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.9 Å) |
Structure validation
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