8IDD

Cryo-EM structure of Mycobacterium tuberculosis ATP bound FtsEX/RipC complex in peptidisc


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Regulation of the cell division hydrolase RipC by the FtsEX system in Mycobacterium tuberculosis.

Li, J.Xu, X.Shi, J.Hermoso, J.A.Sham, L.T.Luo, M.

(2023) Nat Commun 14: 7999-7999

  • DOI: https://doi.org/10.1038/s41467-023-43770-6
  • Primary Citation of Related Structures:  
    8IDB, 8IDC, 8IDD, 8IGQ, 8JIA

  • PubMed Abstract: 

    The FtsEX complex regulates, directly or via a protein mediator depending on bacterial genera, peptidoglycan degradation for cell division. In mycobacteria and Gram-positive bacteria, the FtsEX system directly activates peptidoglycan-hydrolases by a mechanism that remains unclear. Here we report our investigation of Mycobacterium tuberculosis FtsEX as a non-canonical regulator with high basal ATPase activity. The cryo-EM structures of the FtsEX system alone and in complex with RipC, as well as the ATP-activated state, unveil detailed information on the signal transduction mechanism, leading to the activation of RipC. Our findings indicate that RipC is recognized through a "Match and Fit" mechanism, resulting in an asymmetric rearrangement of the extracellular domains of FtsX and a unique inclined binding mode of RipC. This study provides insights into the molecular mechanisms of FtsEX and RipC regulation in the context of a critical human pathogen, guiding the design of drugs targeting peptidoglycan remodeling.


  • Organizational Affiliation

    Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division ATP-binding protein FtsEA [auth B],
E [auth A]
230Mycobacterium tuberculosisMutation(s): 0 
Gene Names: ftsERv3102cRVBD_3102cLH57_16935P425_03233
Membrane Entity: Yes 
UniProt
Find proteins for O05779 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore O05779 
Go to UniProtKB:  O05779
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO05779
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division protein FtsXB [auth D],
C
297Mycobacterium tuberculosisMutation(s): 0 
Gene Names: ftsX
Membrane Entity: Yes 
UniProt
Find proteins for P9WG19 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WG19 
Go to UniProtKB:  P9WG19
Entity Groups  
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UniProt GroupP9WG19
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Probable endopeptidase MT2245D [auth E]385Mycobacterium tuberculosisMutation(s): 0 
Gene Names: MT2245
EC: 3.4
UniProt
Find proteins for P9WHU3 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHU3 
Go to UniProtKB:  P9WHU3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WHU3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
F [auth B],
G [auth A]
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Education (MoE, Singapore)SingaporeA-0008412-00-00

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-04
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Database references