3WDE

Mutant N-terminal domain of Mycobacterium tuberculosis ClpC1, F80Y, bound to Cyclomarin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.127 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of mycobacterial inhibition by cyclomarin A

Vasudevan, D.Rao, S.P.S.Noble, C.G.

(2013) J.Biol.Chem. 288: 30883-30891

  • DOI: 10.1074/jbc.M113.493767
  • Primary Citation of Related Structures:  3WDB, 3WDC, 3WDD

  • PubMed Abstract: 
  • Cyclomarin A (CymA) was identified as a mycobactericidal compound targeting ClpC1. However, the target was identified based on pulldown experiments and in vitro binding data, without direct functional evidence in mycobacteria. Here we show that CymA ...

    Cyclomarin A (CymA) was identified as a mycobactericidal compound targeting ClpC1. However, the target was identified based on pulldown experiments and in vitro binding data, without direct functional evidence in mycobacteria. Here we show that CymA specifically binds to the N-terminal domain of ClpC1. In addition we have determined the co-crystal structure of CymA bound to the N-terminal domain of ClpC1 to high resolution. Based on the structure of the complex several mutations were engineered into ClpC1, which showed reduced CymA binding in vitro. The ClpC1 mutants were overexpressed in mycobacteria and two showed resistance to CymA, providing the first direct evidence that ClpC1 is the target of CymA. Phe(80) is important in vitro and in cells for the ClpC1-CymA interaction and this explains why other bacteria are resistant to CymA. A model for how CymA binding to the N-terminal domain of ClpC1 leads to uncontrolled proteolysis by the associated ClpP protease machinery is discussed.


    Organizational Affiliation

    From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore 138670.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable ATP-dependent Clp protease ATP-binding subunit
A
153Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Gene Names: clpC1
Find proteins for P9WPC9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WPC9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cyclomarin A
B
7N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001124
Query on PRD_001124
BCyclomarin ACyclic peptide / Antiinflammatory

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.127 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 34.020α = 90.00
b = 58.860β = 90.00
c = 63.990γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-09-18
    Type: Initial release
  • Version 1.1: 2013-12-11
    Type: Database references