4JK1

X-ray crystal structure of Escherichia coli sigma70 holoenzyme in complex with Guanosine tetraphosphate (ppGpp)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.255 

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This is version 1.3 of the entry. See complete history


Literature

Differential regulation by ppGpp versus pppGpp in Escherichia coli.

Mechold, U.Potrykus, K.Murphy, H.Murakami, K.S.Cashel, M.

(2013) Nucleic Acids Res 41: 6175-6189

  • DOI: https://doi.org/10.1093/nar/gkt302
  • Primary Citation of Related Structures:  
    4JK1, 4JK2

  • PubMed Abstract: 

    Both ppGpp and pppGpp are thought to function collectively as second messengers for many complex cellular responses to nutritional stress throughout biology. There are few indications that their regulatory effects might be different; however, this question has been largely unexplored for lack of an ability to experimentally manipulate the relative abundance of ppGpp and pppGpp. Here, we achieve preferential accumulation of either ppGpp or pppGpp with Escherichia coli strains through induction of different Streptococcal (p)ppGpp synthetase fragments. In addition, expression of E. coli GppA, a pppGpp 5'-gamma phosphate hydrolase that converts pppGpp to ppGpp, is manipulated to fine tune differential accumulation of ppGpp and pppGpp. In vivo and in vitro experiments show that pppGpp is less potent than ppGpp with respect to regulation of growth rate, RNA/DNA ratios, ribosomal RNA P1 promoter transcription inhibition, threonine operon promoter activation and RpoS induction. To provide further insights into regulation by (p)ppGpp, we have also determined crystal structures of E. coli RNA polymerase-σ(70) holoenzyme with ppGpp and pppGpp. We find that both nucleotides bind to a site at the interface between β' and ω subunits.


  • Organizational Affiliation

    Laboratory of Molecular Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Escherichia coli RNA polymerase alpha subunitA,
B,
G [auth F],
H [auth G]
329Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoApezphssezb3295JW3257
EC: 2.7.7.6
UniProt
Find proteins for P0A7Z4 (Escherichia coli (strain K12))
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UniProt GroupP0A7Z4
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Escherichia coli RNA polymerase beta subunitC,
I [auth H]
1,342Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoBgroNnitBrifronstlstvtabDb3987JW3950
EC: 2.7.7.6
UniProt
Find proteins for P0A8V2 (Escherichia coli (strain K12))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Escherichia coli RNA polymerase beta' subunitD,
J [auth I]
1,407Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoCtabBb3988JW3951
EC: 2.7.7.6
UniProt
Find proteins for P0A8T7 (Escherichia coli (strain K12))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Escherichia coli RNA polymerase omega subunitE,
K [auth J]
91Escherichia coli str. K-12 substr. MDS42Mutation(s): 0 
Gene Names: rpoZECMDS42_3083
EC: 2.7.7.6
UniProt
Find proteins for P0A800 (Escherichia coli (strain K12))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Escherichia coli RNA polymerase sigma70 subunitF [auth X],
L [auth Y]
613Escherichia coli K-12Mutation(s): 0 
Gene Names: rpoDaltb3067JW3039
UniProt
Find proteins for P00579 (Escherichia coli (strain K12))
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.90 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.255 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 184.567α = 90
b = 203.817β = 90
c = 307.674γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-04-10
    Type: Initial release
  • Version 1.1: 2013-06-19
    Changes: Database references
  • Version 1.2: 2013-07-17
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Structure summary