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: 4.5 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.264 

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
  • Primary Citation of Related Structures:  

  • 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 ATPase
A, B, C, D, E, F, J, K, L, M, N, O
251Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: mpa
Find proteins for P9WQN5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WQN5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Prokaryotic ubiquitin-like protein pup
G, H, I, P, Q, R
68Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 1 
Gene Names: pup
Find proteins for P9WHN5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WHN5
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.5 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.264 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 176.580α = 90.00
b = 176.960β = 89.94
c = 176.610γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHENIXmodel building
HKL-2000data collection
SCALAdata scaling
PHENIXphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance