1ZYR

Structure of Thermus thermophilus RNA polymerase holoenzyme in complex with the antibiotic streptolydigin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.261 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation.

Tuske, S.Sarafianos, S.G.Wang, X.Hudson, B.Sineva, E.Mukhopadhyay, J.Birktoft, J.J.Leroy, O.Ismail, S.Clark, A.D.Dharia, C.Napoli, A.Laptenko, O.Lee, J.Borukhov, S.Ebright, R.H.Arnold, E.

(2005) Cell 122: 541-552

  • DOI: 10.1016/j.cell.2005.07.017
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We define the target, mechanism, and structural basis of inhibition of bacterial RNA polymerase (RNAP) by the tetramic acid antibiotic streptolydigin (Stl). Stl binds to a site adjacent to but not overlapping the RNAP active center and stabilizes an ...

    We define the target, mechanism, and structural basis of inhibition of bacterial RNA polymerase (RNAP) by the tetramic acid antibiotic streptolydigin (Stl). Stl binds to a site adjacent to but not overlapping the RNAP active center and stabilizes an RNAP-active-center conformational state with a straight-bridge helix. The results provide direct support for the proposals that alternative straight-bridge-helix and bent-bridge-helix RNAP-active-center conformations exist and that cycling between straight-bridge-helix and bent-bridge-helix RNAP-active-center conformations is required for RNAP function. The results set bounds on models for RNAP function and suggest strategies for design of novel antibacterial agents.


    Organizational Affiliation

    Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase alpha chain
A, B, K, L
315Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
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 beta chain
C, M
1119Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
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' chain
D, N
1524Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
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 omega chain
E, O
99Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for Q8RQE7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q8RQE7
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase sigma chain
F, P
423Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: sigA
Find proteins for Q5SKW1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SKW1
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
D, M
STREPTOLYDIGIN
2-PYRROLIDINEACETAMIDE, 4-[6-(1,4-DIMETHYLSPIRO[2,9-DIOXABICYCLO[3.3.1]NON-6-ENE-8,2'-OXIRAN-3-YL)-1-HYDROXY-4-METHYL-2,4-HEPTADIENYLIDENE]-N,ALPHA-DIMETHYL-3,5-DIOXO-1-(TETRAHYDRO-5-HYDROXY-6-METHYL-2H-PYRAN-2-YL)-; PORTAMYCIN
C32 H44 N2 O9
KVTPRMVXYZKLIG-NCAOFHFGSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
D, N
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
STDKi: 1800 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.261 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 237.000α = 90.00
b = 237.000β = 90.00
c = 250.000γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
HKL-2000data collection
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-09-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance