5D4E: Crystal Structure Of Thermus Thermophilus Product Complex For Transcription Initiation With 3'-dephosphate-coa And Ctp

Citation:
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.
PDB ID: 5D4EDownload
MMDB ID: 140873
PDB Deposition Date: 2015/8/7
Updated in MMDB: 2016/08
Experimental Method:
x-ray diffraction
Resolution: 3.08  Å
Source Organism:
Thermus thermophilus HB8
Similar Structures:
Biological Unit for 5D4E: octameric; determined by author and by software (PISA)
Molecular Components in 5D4E
Label Count Molecule
Proteins (6 molecules)
2
DNA-directed RNA Polymerase Subunit Alpha
Molecule annotation
1
DNA-directed RNA Polymerase Subunit Beta(Gene symbol: rpoB)
Molecule annotation
1
DNA-directed RNA Polymerase Subunit Beta'(Gene symbol: TTHA1812)
Molecule annotation
1
DNA-directed RNA Polymerase Subunit Omega(Gene symbol: rpoZ)
Molecule annotation
1
RNA Polymerase Sigma Factor Siga
Molecule annotation
Nucleotides(2 molecules)
1
DNA (27-mer)
Molecule annotation
1
DNA (5'- D(*cp*c*tp*gp*cp*ap*tp*cp*cp*gp*tp*gp*ap*gp*tp*ap*gp*ap*g)-3')
Molecule annotation
Chemicals (10 molecules)
1
5
2
2
3
1
4
1
5
1
* Click molecule labels to explore molecular sequence information.

Citing MMDB
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