4OIR

Crystal structure of Thermus thermophilus RNA polymerase transcription initiation complex soaked with GE23077 and rifamycin SV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

GE23077 binds to the RNA polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides.

Zhang, Y.Degen, D.Ho, M.X.Sineva, E.Ebright, K.Y.Ebright, Y.W.Mekler, V.Vahedian-Movahed, H.Feng, Y.Yin, R.Tuske, S.Irschik, H.Jansen, R.Maffioli, S.Donadio, S.Arnold, E.Ebright, R.H.

(2014) Elife 3: e02450-e02450

  • DOI: https://doi.org/10.7554/eLife.02450
  • Primary Citation of Related Structures:  
    4MQ9, 4OIN, 4OIO, 4OIP, 4OIQ, 4OIR

  • PubMed Abstract: 

    Using a combination of genetic, biochemical, and structural approaches, we show that the cyclic-peptide antibiotic GE23077 (GE) binds directly to the bacterial RNA polymerase (RNAP) active-center 'i' and 'i+1' nucleotide binding sites, preventing the binding of initiating nucleotides, and thereby preventing transcription initiation. The target-based resistance spectrum for GE is unusually small, reflecting the fact that the GE binding site on RNAP includes residues of the RNAP active center that cannot be substituted without loss of RNAP activity. The GE binding site on RNAP is different from the rifamycin binding site. Accordingly, GE and rifamycins do not exhibit cross-resistance, and GE and a rifamycin can bind simultaneously to RNAP. The GE binding site on RNAP is immediately adjacent to the rifamycin binding site. Accordingly, covalent linkage of GE to a rifamycin provides a bipartite inhibitor having very high potency and very low susceptibility to target-based resistance. DOI: http://dx.doi.org/10.7554/eLife.02450.001.


  • Organizational Affiliation

    Waksman Institute, Rutgers University, Piscataway, United States.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alpha
A, B
305Thermus thermophilus HB8Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q5SHR6 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Go to UniProtKB:  Q5SHR6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5SHR6
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta1,119Thermus thermophilus HB8Mutation(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 thermophilus HB8Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE8 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Entity Groups  
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UniProt GroupQ8RQE8
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omega99Thermus thermophilus HB8Mutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for Q8RQE7 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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UniProt GroupQ8RQE7
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA directed RNA polymerase sigma factor A443Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpoDTTHA0532
UniProt
Find proteins for Q5SKW1 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8))
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Go to UniProtKB:  Q5SKW1
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UniProt GroupQ5SKW1
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  • Reference Sequence

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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
GE230777Actinomadura sp.Mutation(s): 0 
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Entity ID: 6
MoleculeChains LengthOrganismImage
5'-D(*CP*CP*T*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*GP*AP*GP*GP*G)-3'21N/A
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Entity ID: 7
MoleculeChains LengthOrganismImage
5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*GP*CP*AP*GP*G)-3'27N/A
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RFV
Query on RFV

Download Ideal Coordinates CCD File 
K [auth C]rifamycin SV
C37 H49 N O12
OUOULRWGQDSKTQ-ZVFQNIRDSA-N
MB8
Query on MB8

Download Ideal Coordinates CCD File 
Q [auth I](2Z)-2-methylbut-2-enoic acid
C5 H8 O2
UIERETOOQGIECD-ARJAWSKDSA-N
ZN
Query on ZN

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L [auth D],
M [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

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J [auth B],
N [auth D],
O [auth D],
P [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
2RA
Query on 2RA
I
D-PEPTIDE LINKINGC3 H8 N2 O2ALA
FGL
Query on FGL
I
L-PEPTIDE LINKINGC3 H5 N O4GLY
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.7α = 90
b = 105.01β = 98.79
c = 295.36γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
MOLREPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-07
    Type: Initial release
  • Version 1.1: 2014-05-14
    Changes: Non-polymer description
  • Version 1.2: 2023-09-20
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description