6OVY

X-ray crystal structure of a bacterial reiterative transcription complex of pyrG promoter variant -1C


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


Literature

Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase.

Shin, Y.Hedglin, M.Murakami, K.S.

(2020) Nucleic Acids Res 48: 2144-2155

  • DOI: https://doi.org/10.1093/nar/gkz1221
  • Primary Citation of Related Structures:  
    6OVR, 6OVY, 6OW3, 6OY5, 6OY6, 6OY7, 6P70, 6P71

  • PubMed Abstract: 

    Reiterative transcription is a non-canonical form of RNA synthesis by RNA polymerase in which a ribonucleotide specified by a single base in the DNA template is repetitively added to the nascent RNA transcript. We previously determined the X-ray crystal structure of the bacterial RNA polymerase engaged in reiterative transcription from the pyrG promoter, which contains eight poly-G RNA bases synthesized using three C bases in the DNA as a template and extends RNA without displacement of the promoter recognition σ factor from the core enzyme. In this study, we determined a series of transcript initiation complex structures from the pyrG promoter using soak-trigger-freeze X-ray crystallography. We also performed biochemical assays to monitor template DNA translocation during RNA synthesis from the pyrG promoter and in vitro transcription assays to determine the length of poly-G RNA from the pyrG promoter variants. Our study revealed how RNA slips on template DNA and how RNA polymerase and template DNA determine length of reiterative RNA product. Lastly, we determined a structure of a transcript initiation complex at the pyrBI promoter and proposed an alternative mechanism of RNA slippage and extension requiring the σ dissociation from the core enzyme.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Center for RNA Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B
315Thermus thermophilusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5SHR6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ5SHR6
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,119Thermus thermophilusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE9 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ8RQE9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'1,524Thermus thermophilusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ8RQE8
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega99Thermus thermophilusMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
RNA polymerase sigma factor SigA423Thermus thermophilusMutation(s): 0 
UniProt
Find proteins for Q5SKW1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ5SKW1
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  • Reference Sequence

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Entity ID: 6
MoleculeChains LengthOrganismImage
DNA (5'-D(P*CP*AP*TP*CP*AP*GP*AP*GP*CP*CP*CP*CP*AP*AP*A)-3')22Bacillus subtilis
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Entity ID: 7
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*TP*CP*TP*GP*AP*TP*G)-3')27Bacillus subtilis
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Entity ID: 8
MoleculeChains LengthOrganismImage
RNA (5'-D(*(GTP))-R(P*GP*GP*G)-3')4Thermus thermophilus
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.83α = 90
b = 102.479β = 98.8
c = 295.596γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM087350

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.2: 2020-02-05
    Changes: Database references
  • Version 1.3: 2020-03-11
    Changes: Database references
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description