5KWA

complete structure of the Mycobacterium tuberculosis proteasomal ATPase Mpa

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

  • Deposited: 2016-07-17 Released: 2017-06-07 
  • Deposition Author(s): Wang, T., WU, Y.J.
  • Funding Organization(s): Ministry of Science and Technology, National Natural Science Foundation of China, shenzhen science and technology innovation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Mycobacterium tuberculosis proteasomal ATPase Mpa has a beta-grasp domain that hinders docking with the proteasome core protease

Wu, Y.Hu, K.Li, D.Bai, L.Yang, S.Jastrab, J.B.Xiao, S.Hu, Y.Zhang, S.Darwin, K.H.Wang, T.Li, H.

(2017) Mol Microbiol 105: 227-241

  • DOI: 10.1111/mmi.13695
  • Primary Citation of Related Structures:  
    5KWA, 5KZF

  • PubMed Abstract: 
  • Mycobacterium tuberculosis (Mtb) has a proteasome system that is essential for its ability to cause lethal infections in mice. A key component of the system is the proteasomal adenosine triphosphatase (ATPase) Mpa, which captures, unfolds, and translocates protein substrates into the Mtb proteasome core particle for degradation ...

    Mycobacterium tuberculosis (Mtb) has a proteasome system that is essential for its ability to cause lethal infections in mice. A key component of the system is the proteasomal adenosine triphosphatase (ATPase) Mpa, which captures, unfolds, and translocates protein substrates into the Mtb proteasome core particle for degradation. Here, we report the crystal structures of near full-length hexameric Mtb Mpa in apo and ADP-bound forms. Surprisingly, the structures revealed a ubiquitin-like β-grasp domain that precedes the proteasome-activating carboxyl terminus. This domain, which was only found in bacterial proteasomal ATPases, buries the carboxyl terminus of each protomer in the central channel of the hexamer and hinders the interaction of Mpa with the proteasome core protease. Thus, our work reveals the structure of a bacterial proteasomal ATPase in the hexameric form, and the structure finally explains why Mpa is unable to stimulate robust protein degradation in vitro in the absence of other, yet-to-be-identified co-factors.


    Organizational Affiliation

    Cryo-EM Structural Biology Laboratory, Van Andel Research Institute, Grand Rapids, MI, 49503, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Proteasome-associated ATPaseA, B497Mycobacterium tuberculosisMutation(s): 0 
Gene Names: mpaERS007663_01871
UniProt
Find proteins for P9WQN5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WQN5 
Go to UniProtKB:  P9WQN5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WQN5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
C [auth A],
E [auth B]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.230 
  • Space Group: P 3 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.931α = 90
b = 111.931β = 90
c = 196.072γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-07-17 
  • Released Date: 2017-06-07 
  • Deposition Author(s): Wang, T., WU, Y.J.

Funding OrganizationLocationGrant Number
Ministry of Science and TechnologyChina2013CB911500
National Natural Science Foundation of ChinaChina31300600
shenzhen science and technology innovationChinaJCYJ20160331115853521

Revision History  (Full details and data files)

  • Version 1.0: 2017-06-07
    Type: Initial release
  • Version 1.1: 2017-07-19
    Changes: Database references
  • Version 1.2: 2017-10-18
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-04
    Changes: Data collection