6BYU

X-ray crystal structure of Escherichia coli RNA polymerase (RpoB-H526Y) and ppApp complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.244 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structure-function comparisons of (p)ppApp vs (p)ppGpp for Escherichia coli RNA polymerase binding sites and for rrnB P1 promoter regulatory responses in vitro.

Bruhn-Olszewska, B.Molodtsov, V.Sobala, M.Dylewski, M.Murakami, K.S.Cashel, M.Potrykus, K.

(2018) Biochim. Biophys. Acta 1861: 731-742

  • DOI: 10.1016/j.bbagrm.2018.07.005

  • PubMed Abstract: 
  • Precise regulation of gene expression is crucial for bacteria to respond to changing environmental conditions. In addition to protein factors affecting RNA polymerase (RNAP) activity, second messengers play an important role in transcription regulati ...

    Precise regulation of gene expression is crucial for bacteria to respond to changing environmental conditions. In addition to protein factors affecting RNA polymerase (RNAP) activity, second messengers play an important role in transcription regulation, such as well-known effectors of the stringent response: guanosine 5'triphosphate-3'diphosphate and guanosine 3', 5'-bis(diphosphate) [(p)ppGpp]. Although much is known about importance of the 5' and 3' moieties of (p)ppGpp, the role of the guanine base remains somewhat cryptic. Here, we use (p)ppGpp's adenine analogs [(p)ppApp] to investigate how the nucleobase contributes to determine its binding site and transcriptional regulation. We determined X-ray crystal structure of Escherichia coli RNAP-(p)ppApp complex, which shows the analogs bind near the active site and switch regions of RNAP. We have also explored the regulatory effects of (p)ppApp on transcription initiating from the well-studied E. coli rrnB P1 promoter to assess and compare properties of (p)ppApp with (p)ppGpp. We demonstrate that contrary to (p)ppGpp, (p)ppApp activates transcription at this promoter and DksA hinders this effect. Moreover, pppApp exerts a stronger effect than ppApp. We also show that when ppGpp and pppApp are present together, the outcome depends on which one of them was pre-incubated with RNAP first. This behavior suggests a surprising Yin-Yang like reciprocal plasticity of RNAP responses at a single promoter, occasioned simply by pre-exposure to one or the other nucleotide. Our observations underscore the importance of the (p)ppNpp's purine nucleobase for interactions with RNAP, which may lead to a better fundamental understanding of (p)ppGpp regulation of RNAP activity.


    Organizational Affiliation

    Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland. Electronic address: b.bruhn.olszewska@ug.edu.pl.,Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland. Electronic address: michal.sobala@phdstud.edu.pl.,Intramural Research Program, Eunice Kennedy Shriver NICHD, National Institutes of Health, Bethesda, MD 20892, USA. Electronic address: cashelm@mail.nih.gov.,Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland. Electronic address: maciej.dylewski@phdstud.edu.pl.,Department of Biochemistry and Molecular Biology, Center of RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA. Electronic address: kum14@psu.edu.,Department of Biochemistry and Molecular Biology, Center of RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA. Electronic address: vum5@psu.edu.,Department of Bacterial Molecular Genetics, Faculty of Biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland. Electronic address: katarzyna.potrykus@biol.ug.edu.pl.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
A, B, G, H
329Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoA (pez, phs, sez)
EC: 2.7.7.6
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Z4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
C, I
1342Escherichia coli (strain K12)Mutation(s): 1 
Gene Names: rpoB (groN, nitB, rif, ron, stl, stv, tabD)
EC: 2.7.7.6
Find proteins for P0A8V2 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8V2
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
D, J
1407Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoC (tabB)
EC: 2.7.7.6
Find proteins for P0A8T7 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8T7
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
E, K
91Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for P0A800 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A800
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor RpoD
F, L
613Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoD (alt)
Find proteins for P00579 (Escherichia coli (strain K12))
Go to UniProtKB:  P00579
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
D, J
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
D, J
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
ECJ
Query on ECJ

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Download CCD File 
C, I
(5R)-5-(6-amino-9H-purin-9-yl)-2-({[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}methyl)-4-oxo-4,5-dihydrofuran-3-yl trihydrogen diphosphate
C10 H13 N5 O16 P4
CDOGMROMDFBAJR-SNVBAGLBSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.6 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.244 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 186.254α = 90.00
b = 203.656β = 90.00
c = 308.322γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM087350

Revision History 

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-02-14
    Type: Author supporting evidence
  • Version 1.2: 2018-08-01
    Type: Data collection, Database references
  • Version 1.3: 2018-08-15
    Type: Data collection, Source and taxonomy, Structure summary
  • Version 2.0: 2018-08-29
    Type: Atomic model, Data collection, Derived calculations, Source and taxonomy, Structure summary