5D4C

Crystal structure of Thermus thermophilus product complex for transcription initiation with ATP and CTP

Summary for 5D4C

• Entry DOI: 10.2210/pdb5d4c/pdb
• Related: 4G7H 5D4D 5D4E
• Descriptor: DNA-directed RNA polymerase subunit alpha, CYTIDINE-5'-MONOPHOSPHATE, CYTIDINE-5'-TRIPHOSPHATE, ... (13 entities in total)
• Functional Keywords: rna polymerase, transcription initiation, bacterial, ncin, non-canonical initiating nucleotide, primer-dependent initiation, dna, single-stranded, dna-directed rna polymerases, gene expression regulation, promoter regions, genetic, protein conformation, sigma factor, thermus thermophilus, transcription, transcription-dna complex, transcription/dna
• Biological source: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579); More
• Cellular location: Cytoplasm : Q5SKW1
• Total number of polymer chains: 16
• Total formula weight: 889388.44

Authors

Zhang, Y.,Ebright, R.H. (deposition date: 2015-08-07, release date: 2016-07-06, Last modification date: 2024-07-03)

Primary citation

Bird, J.G.,Zhang, Y.,Tian, Y.,Panova, N.,Barvik, I.,Greene, L.,Liu, M.,Buckley, B.,Krasny, L.,Lee, J.K.,Kaplan, C.D.,Ebright, R.H.,Nickels, B.E.
The mechanism of RNA 5' capping with NAD(+), NADH and desphospho-CoA.
Nature, 535:444-447, 2016

PubMed Abstract: The chemical nature of the 5′ end of RNA is a key determinant of RNA stability, processing, localization and translation efficiency, and has been proposed to provide a layer of ‘epitranscriptomic’ gene regulation. Recently it has been shown that some bacterial RNA species carry a 5′-end structure reminiscent of the 5′ 7-methylguanylate ‘cap’ in eukaryotic RNA. In particular, RNA species containing a 5′-end nicotinamide adenine dinucleotide (NAD+) or 3′-desphospho-coenzyme A (dpCoA) have been identified in both Gram-negative and Gram-positive bacteria. It has been proposed that NAD+, reduced NAD+ (NADH) and dpCoA caps are added to RNA after transcription initiation, in a manner analogous to the addition of 7-methylguanylate caps. Here we show instead that NAD+, NADH and dpCoA are incorporated into RNA during transcription initiation, by serving as non-canonical initiating nucleotides (NCINs) for de novo transcription initiation by cellular RNA polymerase (RNAP). We further show that both bacterial RNAP and eukaryotic RNAP II incorporate NCIN caps, that promoter DNA sequences at and upstream of the transcription start site determine the efficiency of NCIN capping, that NCIN capping occurs in vivo, and that NCIN capping has functional consequences. We report crystal structures of transcription initiation complexes containing NCIN-capped RNA products. Our results define the mechanism and structural basis of NCIN capping, and suggest that NCIN-mediated ‘ab initio capping’ may occur in all organisms.

PubMed: 27383794
DOI: 10.1038/nature18622

Experimental method

X-RAY DIFFRACTION (3.28 Å)