5AGU

The sliding clamp of Mycobacterium tuberculosis in complex with a natural product.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.173 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Antibiotics. Targeting Dnan for Tuberculosis Therapy Using Novel Griselimycins.

Kling, A.Lukat, P.Almeida, D.V.Bauer, A.Fontaine, E.Sordello, S.Zaburannyi, N.Herrmann, J.Wenzel, S.C.Konig, C.Ammerman, N.C.Barrio, M.B.Borchers, K.Bordon-Pallier, F.Bronstrup, M.Courtemanche, G.Gerlitz, M.Geslin, M.Hammann, P.Heinz, D.W.Hoffmann, H.Klieber, S.Kohlmann, M.Kurz, M.Lair, C.Matter, H.Nuermberger, E.Tyagi, S.Fraisse, L.Grosset, J.H.Lagrange, S.Muller, R.

(2015) Science 348: 1106

  • DOI: 10.1126/science.aaa4690
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The discovery of Streptomyces-produced streptomycin founded the age of tuberculosis therapy. Despite the subsequent development of a curative regimen for this disease, tuberculosis remains a worldwide problem, and the emergence of multidrug-resistant ...

    The discovery of Streptomyces-produced streptomycin founded the age of tuberculosis therapy. Despite the subsequent development of a curative regimen for this disease, tuberculosis remains a worldwide problem, and the emergence of multidrug-resistant Mycobacterium tuberculosis has prioritized the need for new drugs. Here we show that new optimized derivatives from Streptomyces-derived griselimycin are highly active against M. tuberculosis, both in vitro and in vivo, by inhibiting the DNA polymerase sliding clamp DnaN. We discovered that resistance to griselimycins, occurring at very low frequency, is associated with amplification of a chromosomal segment containing dnaN, as well as the ori site. Our results demonstrate that griselimycins have high translational potential for tuberculosis treatment, validate DnaN as an antimicrobial target, and capture the process of antibiotic pressure-induced gene amplification.


    Organizational Affiliation

    Department of Microbial Natural Products, Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research and Pharmaceutical Biotechnology, Saarland University, 66123 Saarbr├╝cken, Germany. German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Hannover, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA POLYMERASE III SUBUNIT BETA
A, B
406Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: dnaN
Find proteins for P9WNU1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WNU1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
GRISELIMYCIN
C, D
11N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BU3
Query on BU3

Download SDF File 
Download CCD File 
A
(R,R)-2,3-BUTANEDIOL
C4 H10 O2
OWBTYPJTUOEWEK-QWWZWVQMSA-N
 Ligand Interaction
TRS
Query on TRS

Download SDF File 
Download CCD File 
A
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
 Ligand Interaction
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
MLU
Query on MLU
C, D
D-PEPTIDE LINKINGC7 H15 N O2

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NZC
Query on NZC
C, D
L-PEPTIDE LINKINGC5 H11 N O3THR
MVA
Query on MVA
C, D
L-PEPTIDE LINKINGC6 H13 N O2VAL
MP8
Query on MP8
C, D
L-PEPTIDE LINKINGC6 H11 N O2PRO
ACE
Query on ACE
C, D
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.173 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.184 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 87.516α = 90.00
b = 87.516β = 90.00
c = 199.296γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-06-03
    Type: Initial release
  • Version 1.1: 2015-06-17
    Type: Database references
  • Version 1.2: 2016-10-19
    Type: Atomic model, Derived calculations