5X21

Crystal structure of Thermus thermophilus transcription initiation complex with GpA and pseudouridimycin (PUM)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.323 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Antibacterial Nucleoside-Analog Inhibitor of Bacterial RNA Polymerase.

Maffioli, S.I.Zhang, Y.Degen, D.Carzaniga, T.Del Gatto, G.Serina, S.Monciardini, P.Mazzetti, C.Guglierame, P.Candiani, G.Chiriac, A.I.Facchetti, G.Kaltofen, P.Sahl, H.G.Deho, G.Donadio, S.Ebright, R.H.

(2017) Cell 169: 1240-1248.e23

  • DOI: 10.1016/j.cell.2017.05.042
  • Primary Citation of Related Structures:  5X22

  • PubMed Abstract: 
  • Drug-resistant bacterial pathogens pose an urgent public-health crisis. Here, we report the discovery, from microbial-extract screening, of a nucleoside-analog inhibitor that inhibits bacterial RNA polymerase (RNAP) and exhibits antibacterial activit ...

    Drug-resistant bacterial pathogens pose an urgent public-health crisis. Here, we report the discovery, from microbial-extract screening, of a nucleoside-analog inhibitor that inhibits bacterial RNA polymerase (RNAP) and exhibits antibacterial activity against drug-resistant bacterial pathogens: pseudouridimycin (PUM). PUM is a natural product comprising a formamidinylated, N-hydroxylated Gly-Gln dipeptide conjugated to 6'-amino-pseudouridine. PUM potently and selectively inhibits bacterial RNAP in vitro, inhibits bacterial growth in culture, and clears infection in a mouse model of Streptococcus pyogenes peritonitis. PUM inhibits RNAP through a binding site on RNAP (the NTP addition site) and mechanism (competition with UTP for occupancy of the NTP addition site) that differ from those of the RNAP inhibitor and current antibacterial drug rifampin (Rif). PUM exhibits additive antibacterial activity when co-administered with Rif, exhibits no cross-resistance with Rif, and exhibits a spontaneous resistance rate an order-of-magnitude lower than that of Rif. PUM is a highly promising lead for antibacterial therapy.


    Organizational Affiliation

    NAICONS Srl, 20139 Milan, Italy; Vicuron Pharmaceuticals, 21040 Gerenzano, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
A, B
315Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpoA
EC: 2.7.7.6
Find proteins for Q5SHR6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHR6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
C
1119Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpoB
EC: 2.7.7.6
Find proteins for Q8RQE9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q8RQE9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
D
1524Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Gene Names: rpoC
EC: 2.7.7.6
Find proteins for Q8RQE8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q8RQE8
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
E
99Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for Q72ID6 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72ID6
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor SigA
F
443Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Gene Names: sigA (rpoD)
Find proteins for Q72L95 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72L95
Entity ID: 6
MoleculeChainsLengthOrganism
promoter DNA template strandG21Thermus thermophilus
Entity ID: 7
MoleculeChainsLengthOrganism
promoter DNA nontemplate strandH27Thermus thermophilus
Entity ID: 8
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*A)-3')I2Thermus thermophilus
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A, C, D, F, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
PUM
Query on PUM

Download SDF File 
Download CCD File 
I
(1S)-1,4-anhydro-5-[(N-carbamimidoylglycyl-N~2~-hydroxy-L-glutaminyl)amino]-5-deoxy-1-(2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)-D-ribitol
pseudouridimycin
C17 H26 N8 O9
XDEYHXABZOKKDZ-YFKLLHAASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.323 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.232 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 186.790α = 90.00
b = 103.090β = 98.71
c = 296.230γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling
MOLREPphasing
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2017-01-29 
  • Released Date: 2017-07-05 
  • Deposition Author(s): Zhang, Y., Ebright, R.

Revision History 

  • Version 1.0: 2017-07-05
    Type: Initial release
  • Version 1.1: 2018-01-17
    Type: Author supporting evidence