5UHG

Crystal structure of Mycobacterium tuberculosis transcription initiation complex in complex with D-AAP1 and Rifampin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.971 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition.

Lin, W.Mandal, S.Degen, D.Liu, Y.Ebright, Y.W.Li, S.Feng, Y.Zhang, Y.Mandal, S.Jiang, Y.Liu, S.Gigliotti, M.Talaue, M.Connell, N.Das, K.Arnold, E.Ebright, R.H.

(2017) Mol. Cell 66: 169-179.e8

  • DOI: 10.1016/j.molcel.2017.03.001
  • Primary Citation of Related Structures:  5UH5, 5UH6, 5UH7, 5UH8, 5UH9, 5UHA, 5UHB, 5UHC, 5UHD, 5UHE, 5UHF

  • PubMed Abstract: 
  • Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, which kills 1.8 million annually. Mtb RNA polymerase (RNAP) is the target of the first-line antituberculosis drug rifampin (Rif). We report crystal structures of Mtb RNAP, alone ...

    Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, which kills 1.8 million annually. Mtb RNA polymerase (RNAP) is the target of the first-line antituberculosis drug rifampin (Rif). We report crystal structures of Mtb RNAP, alone and in complex with Rif, at 3.8-4.4 Å resolution. The results identify an Mtb-specific structural module of Mtb RNAP and establish that Rif functions by a steric-occlusion mechanism that prevents extension of RNA. We also report non-Rif-related compounds-Nα-aroyl-N-aryl-phenylalaninamides (AAPs)-that potently and selectively inhibit Mtb RNAP and Mtb growth, and we report crystal structures of Mtb RNAP in complex with AAPs. AAPs bind to a different site on Mtb RNAP than Rif, exhibit no cross-resistance with Rif, function additively when co-administered with Rif, and suppress resistance emergence when co-administered with Rif.


    Organizational Affiliation

    Waksman Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
A, B
347Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Gene Names: rpoA
EC: 2.7.7.6
Find proteins for P9WGZ1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WGZ1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
C
1178Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Gene Names: rpoB
EC: 2.7.7.6
Find proteins for P9WGY9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WGY9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
D
1316Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Gene Names: rpoC
EC: 2.7.7.6
Find proteins for P9WGY7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WGY7
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
E
110Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for P9WGY5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WGY5
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor SigA
F
528Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Gene Names: sigA (mysA, rpoD, rpoV)
Find proteins for P9WGI1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WGI1
Entity ID: 6
MoleculeChainsLengthOrganism
DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*AP*GP*CP*TP*GP*TP*CP*AP*CP*GP*GP*AP*TP*G)-3')H23Mycobacterium tuberculosis H37Rv
Entity ID: 7
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*CP*CP*AP*GP*G)-3')G16Mycobacterium tuberculosis H37Rv
Small Molecules
Ligands 4 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
RFP
Query on RFP

Download SDF File 
Download CCD File 
C
RIFAMPICIN
C43 H58 N4 O12
JQXXHWHPUNPDRT-WLSIYKJHSA-N
 Ligand Interaction
88G
Query on 88G

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Download CCD File 
D
Nalpha-(benzenecarbonyl)-N-(2-methylphenyl)-D-phenylalaninamide
C23 H22 N2 O2
BMOOQDWJJBWBKZ-OAQYLSRUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.971 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.223 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 151.434α = 90.00
b = 162.147β = 90.00
c = 194.316γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
PHENIXphasing
DENZOdata reduction
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-04-12
    Type: Initial release
  • Version 1.1: 2017-04-26
    Type: Database references
  • Version 1.2: 2017-05-03
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Refinement description