6CUU

Thermus thermophiles RNA polymerase in complex with promoter DNA and antibiotic Kanglemycin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mode of Action of Kanglemycin A, an Ansamycin Natural Product that Is Active against Rifampicin-Resistant Mycobacterium tuberculosis.

Mosaei, H.Molodtsov, V.Kepplinger, B.Harbottle, J.Moon, C.W.Jeeves, R.E.Ceccaroni, L.Shin, Y.Morton-Laing, S.Marrs, E.C.L.Wills, C.Clegg, W.Yuzenkova, Y.Perry, J.D.Bacon, J.Errington, J.Allenby, N.E.E.Hall, M.J.Murakami, K.S.Zenkin, N.

(2018) Mol Cell 72: 263-274.e5

  • DOI: 10.1016/j.molcel.2018.08.028
  • Primary Citation of Related Structures:  
    6CUX, 6CUU

  • PubMed Abstract: 
  • Antibiotic-resistant bacterial pathogens pose an urgent healthcare threat, prompting a demand for new medicines. We report the mode of action of the natural ansamycin antibiotic kanglemycin A (KglA). KglA binds bacterial RNA polymerase at the rifampicin-binding pocket but maintains potency against RNA polymerases containing rifampicin-resistant mutations ...

    Antibiotic-resistant bacterial pathogens pose an urgent healthcare threat, prompting a demand for new medicines. We report the mode of action of the natural ansamycin antibiotic kanglemycin A (KglA). KglA binds bacterial RNA polymerase at the rifampicin-binding pocket but maintains potency against RNA polymerases containing rifampicin-resistant mutations. KglA has antibiotic activity against rifampicin-resistant Gram-positive bacteria and multidrug-resistant Mycobacterium tuberculosis (MDR-M. tuberculosis). The X-ray crystal structures of KglA with the Escherichia coli RNA polymerase holoenzyme and Thermus thermophilus RNA polymerase-promoter complex reveal an altered-compared with rifampicin-conformation of KglA within the rifampicin-binding pocket. Unique deoxysugar and succinate ansa bridge substituents make additional contacts with a separate, hydrophobic pocket of RNA polymerase and preclude the formation of initial dinucleotides, respectively. Previous ansa-chain modifications in the rifamycin series have proven unsuccessful. Thus, KglA represents a key starting point for the development of a new class of ansa-chain derivatized ansamycins to tackle rifampicin resistance.


    Organizational Affiliation

    Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, UK. Electronic address: n.zenkin@ncl.ac.uk.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit alphaA, B315Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpoATT_C1300
EC: 2.7.7.6
Find proteins for Q72I32 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Explore Q72I32 
Go to UniProtKB:  Q72I32
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit betaC1119Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpoBTT_C1461
EC: 2.7.7.6
Find proteins for Q72HM5 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Explore Q72HM5 
Go to UniProtKB:  Q72HM5
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit beta'D1524Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpoCTT_C1460
EC: 2.7.7.6
Find proteins for Q72HM6 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Explore Q72HM6 
Go to UniProtKB:  Q72HM6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase subunit omegaE99Thermus thermophilus HB27Mutation(s): 0 
Gene Names: rpoZTT_C1196
EC: 2.7.7.6
Find proteins for Q72ID6 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Explore Q72ID6 
Go to UniProtKB:  Q72ID6
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase sigma factor SigAF423Thermus thermophilus HB27Mutation(s): 0 
Gene Names: sigArpoDTT_C0164
Find proteins for Q72L95 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Explore Q72L95 
Go to UniProtKB:  Q72L95
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 6
MoleculeChainsLengthOrganismImage
DNA (5'-D(P*TP*GP*CP*AP*TP*CP*AP*GP*AP*GP*CP*CP*CP*AP*AP*AP*A)-3')G22Bacillus subtilis
Find similar nucleic acids by:  (by identity cutoff)  |  Structure
Entity ID: 7
MoleculeChainsLengthOrganismImage
DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*CP*TP*CP*TP*GP*AP*TP*GP*CP*A)-3')H27Bacillus subtilis
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KNG
Query on KNG

Download Ideal Coordinates CCD File 
I [auth C]Kanglemycin A
C50 H67 N O19
RKRZBNCHQZDJPK-UAXKWEMASA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
J [auth D], K [auth D]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
L [auth D], M [auth D]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 185.221α = 90
b = 101.315β = 98.89
c = 294.279γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom102851
Leverhulme TrustUnited KingdomPLP-2014-229
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM087350

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-25
    Type: Initial release
  • Version 1.1: 2018-10-03
    Changes: Data collection, Database references
  • Version 1.2: 2018-10-31
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence