3M9D

Crystal structure of the prokaryotic ubiquintin-like protein Pup complexed with the hexameric proteasomal ATPase Mpa which includes the amino terminal coiled coil domain and the inter domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.265 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Binding-induced folding of prokaryotic ubiquitin-like protein on the Mycobacterium proteasomal ATPase targets substrates for degradation.

Wang, T.Darwin, K.H.Li, H.

(2010) Nat Struct Mol Biol 17: 1352-1357

  • DOI: 10.1038/nsmb.1918
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Mycobacterium tuberculosis uses a proteasome system that is analogous to the eukaryotic ubiquitin-proteasome pathway and is required for pathogenesis. However, the bacterial analog of ubiquitin, prokaryotic ubiquitin-like protein (Pup), is an intrins ...

    Mycobacterium tuberculosis uses a proteasome system that is analogous to the eukaryotic ubiquitin-proteasome pathway and is required for pathogenesis. However, the bacterial analog of ubiquitin, prokaryotic ubiquitin-like protein (Pup), is an intrinsically disordered protein that bears little sequence or structural resemblance to the highly structured ubiquitin. Thus, it was unknown how pupylated proteins were recruited to the proteasome. Here, we show that the Mycobacterium proteasomal ATPase (Mpa) has three pairs of tentacle-like coiled coils that recognize Pup. Mpa bound unstructured Pup through hydrophobic interactions and a network of hydrogen bonds, leading to the formation of an α-helix in Pup. Our work describes a binding-induced folding recognition mechanism in the Pup-proteasome system that differs mechanistically from substrate recognition in the ubiquitin-proteasome system. This key difference between the prokaryotic and eukaryotic systems could be exploited for the development of a small molecule-based treatment for tuberculosis.


    Organizational Affiliation

    Biology Department, Brookhaven National Laboratory, Upton, New York, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Proteasome-associated ATPaseA, B, C, D, E, F, J, K, L, M, N, O251Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: mpaMT2175Rv2115cMTCY261.11c
Find proteins for P9WQN5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WQN5 
Go to UniProtKB:  P9WQN5
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Prokaryotic ubiquitin-like protein pupG, H, I, P, Q, R68Mycobacterium tuberculosis H37RvMutation(s): 1 
Gene Names: pupMT2171Rv2111c
Find proteins for P9WHN5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHN5 
Go to UniProtKB:  P9WHN5
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.50 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.265 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 176.58α = 90
b = 176.96β = 89.94
c = 176.61γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2010-03-22 
  • Released Date: 2010-10-27 
  • Deposition Author(s): Li, H., Wang, T.

Revision History 

  • Version 1.0: 2010-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance