3HF9

Crystal Structure of Mycobacterium Tuberculosis Proteasome open-gate mutant modified by inhibitor GL1

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


This is version 1.2 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:  
    3H6I, 3H6F, 3HFA, 3HF9

  • 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 state b ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome (Alpha subunit) PrcA1, 3, A, B, D, F, I, K, 1,  3,  A,  B,  D,  F,  I,  K,  M,  O,  Q,  S,  U,  W,  Y,  a,  b,  d,  f,  i,  k,  m,  o,  q,  s,  u,  w,  y
240Mycobacterium tuberculosisMutation(s): 0 
Gene Names: prcA, Rv2109c
EC: 3.4.25.1
Find proteins for P9WHU1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHU1 
Go to UniProtKB:  P9WHU1
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome (Beta subunit) PrcB2, 4, C, E, G, H, J, L, 2,  4,  C,  E,  G,  H,  J,  L,  N,  P,  R,  T,  V,  X,  Z,  c,  e,  g,  h,  j,  l,  n,  p,  r,  t,  v,  x,  z
240Mycobacterium tuberculosisMutation(s): 0 
Gene Names: MT2170, prcB, Rv2110c
EC: 3.4.25.1
Find proteins for P9WHU1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHU1 
Go to UniProtKB:  P9WHU1
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.267 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.583α = 90
b = 209.615β = 102.01
c = 284.933γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
CNSrefinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2009-05-11 
  • Released Date: 2009-09-15 
    • Deposition Author(s): Li, D., Li, H.

Revision History 

  • Version 1.0: 2009-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description