7K1V

Partial open state of Mycobacterium tuberculosis zinc metalloprotease 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural analysis of Mycobacterium tuberculosis M13 metalloprotease Zmp1 open states.

Liang, W.G.Mancl, J.M.Zhao, M.Tang, W.J.

(2021) Structure 29: 709

  • DOI: https://doi.org/10.1016/j.str.2020.12.002
  • Primary Citation of Related Structures:  
    6XLY, 7K1V

  • PubMed Abstract: 

    Zinc metalloprotease 1 (Zmp1), a Mycobacterium tuberculosis 75 kDa secreted enzyme, mediates key stages of tuberculosis disease progression. The biological activity of Zmp1 presumably stems from its ability to degrade bacterium- and/or host-derived peptides. The crystal structures of Zmp1 and related M13 metalloproteases, such as neprilysin and endothelin-converting enzyme-1 were determined only in the closed conformation, which cannot capture substrates or release proteolytic products. Thus, the mechanisms of substrate binding and selectivity remain elusive. Here we report two open-state cryo-EM structures of Zmp1, revealed by our SAXS analysis to be the dominant states in solution. Our structural analyses reveal how ligand binding induces a conformational switch in four linker regions to drive the rigid body motion of the D1 and D2 domains, which form the sizable catalytic chamber. Furthermore, they offer insights into the catalytic cycle and mechanism of substrate recognition of M13 metalloproteases for future therapeutic innovations.


  • Organizational Affiliation

    Ben May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Zinc metalloprotease698Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: 
EC: 3.4.24
UniProt
Find proteins for I6X8R2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore I6X8R2 
Go to UniProtKB:  I6X8R2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupI6X8R2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesR01 GM121964

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-23
    Type: Initial release
  • Version 1.1: 2021-01-20
    Changes: Database references
  • Version 1.2: 2021-07-14
    Changes: Database references
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references, Refinement description