3H6I

Crystal Structure of Mycobacterium Tuberculosis Proteasome Modified by inhibitor GL1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Inhibitors selective for mycobacterial versus human proteasomes.

Lin, G.Li, D.de Carvalho, L.P.Deng, H.Tao, H.Vogt, G.Wu, K.Schneider, J.Chidawanyika, T.Warren, J.D.Li, H.Nathan, C.

(2009) Nature 461: 621-626

  • DOI: 10.1038/nature08357
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Many anti-infectives inhibit the synthesis of bacterial proteins, but none selectively inhibits their degradation. Most anti-infectives kill replicating pathogens, but few preferentially kill pathogens that have been forced into a non-replicating sta ...

    Many anti-infectives inhibit the synthesis of bacterial proteins, but none selectively inhibits their degradation. Most anti-infectives kill replicating pathogens, but few preferentially kill pathogens that have been forced into a non-replicating state by conditions in the host. To explore these alternative approaches we sought selective inhibitors of the proteasome of Mycobacterium tuberculosis. Given that the proteasome structure is extensively conserved, it is not surprising that inhibitors of all chemical classes tested have blocked both eukaryotic and prokaryotic proteasomes, and no inhibitor has proved substantially more potent on proteasomes of pathogens than of their hosts. Here we show that certain oxathiazol-2-one compounds kill non-replicating M. tuberculosis and act as selective suicide-substrate inhibitors of the M. tuberculosis proteasome by cyclocarbonylating its active site threonine. Major conformational changes protect the inhibitor-enzyme intermediate from hydrolysis, allowing formation of an oxazolidin-2-one and preventing regeneration of active protease. Residues outside the active site whose hydrogen bonds stabilize the critical loop before and after it moves are extensively non-conserved. This may account for the ability of oxathiazol-2-one compounds to inhibit the mycobacterial proteasome potently and irreversibly while largely sparing the human homologue.


    Organizational Affiliation

    Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York 10065, USA. gal2005@med.cornell.edu




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasome (Alpha subunit) PrcA
A, B, D, F, I, K, M, O, Q, S, U, W, Y, 1
248Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: prcA
EC: 3.4.25.1
Find proteins for P9WHU1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHU1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Proteasome (Beta subunit) PrcB
C, E, G, H, J, L, N, P, R, T, V, X, Z, 2
240Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: prcB
EC: 3.4.25.1
Find proteins for P9WHT9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHT9
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DMF
Query on DMF

Download SDF File 
Download CCD File 
1, 2, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z
DIMETHYLFORMAMIDE
C3 H7 N O
ZMXDDKWLCZADIW-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
OZT
Query on OZT
2, C, E, G, H, J, L, N, P, R, T, V, X, Z
L-peptide NH3 amino terminusC5 H7 N O4

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.43 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 171.615α = 90.00
b = 117.667β = 113.65
c = 196.335γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CBASSdata collection
CNSphasing
HKL-2000data reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2009-04-23 
  • Released Date: 2009-09-15 
  • Deposition Author(s): Li, D., Li, H., Lin, G.

Revision History 

  • Version 1.0: 2009-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance