3WDB | pdb_00003wdb

N-terminal domain of Mycobacterium tuberculosis ClpC1

• PDB DOI: https://doi.org/10.2210/pdb3WDB/pdb

• Classification: CHAPERONE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-06-14 Released: 2013-09-18 
• Deposition Author(s): Vasudevan, D., Noble, C.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 
  0.182 (Depositor), 0.178 (DCC) 
• R-Value Work: 
  0.143 (Depositor), 0.139 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: experimental

Literature

Structural basis of mycobacterial inhibition by cyclomarin A

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

(2013) J Biological Chem 288: 30883-30891

• PubMed: 24022489 
• DOI: https://doi.org/10.1074/jbc.M113.493767
• Primary Citation Related Structures: 
  3WDB, 3WDC, 3WDD, 3WDE


• 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 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.

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Organizational Affiliation: 
• From the Novartis Institute for Tropical Diseases, 05-01 Chromos, Singapore 138670.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 16.46 kDa 
• Atom Count: 1,391 
• Modeled Residue Count: 149 
• Deposited Residue Count: 150 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ATP-dependent Clp protease ATP-binding subunit	A	150	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: clpC
UniProt
Find proteins for P9WPC9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WPC9  Go to UniProtKB:  P9WPC9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	B [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free:  0.182 (Depositor), 0.178 (DCC) 
• R-Value Work:  0.143 (Depositor), 0.139 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.37	α = 90
b = 57.15	β = 90
c = 65.02	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-18 
Deposition Author(s): Vasudevan, D., Noble, C.G.

Revision History  

• Version 1.0: 2013-09-18
  Type: Initial release
  
• Version 1.1: 2013-12-11
  Changes: Database references
• Version 1.2: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description