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- PDB-8idd: Cryo-EM structure of Mycobacterium tuberculosis ATP bound FtsEX/R... -

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Basic information

Entry
Database: PDB / ID: 8idd
TitleCryo-EM structure of Mycobacterium tuberculosis ATP bound FtsEX/RipC complex in peptidisc
Components
  • Cell division ATP-binding protein FtsE
  • Cell division protein FtsX
  • Probable endopeptidase MT2245
KeywordsTRANSPORT PROTEIN / complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / transmembrane transporter activity / cysteine-type peptidase activity / transmembrane transport / manganese ion binding / cell cycle / cell division / magnesium ion binding / ATP hydrolysis activity / proteolysis ...Hydrolases; Acting on peptide bonds (peptidases) / transmembrane transporter activity / cysteine-type peptidase activity / transmembrane transport / manganese ion binding / cell cycle / cell division / magnesium ion binding / ATP hydrolysis activity / proteolysis / ATP binding / plasma membrane
Similarity search - Function
: / Cell division protein FtsE, ATP-binding / NlpC/P60 domain profile. / Cell division protein FtsX / FtsX, extracellular domain / FtsX extracellular domain / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / ABC transporter, lipoprotein release, LolD / ABC3 transporter permease protein domain ...: / Cell division protein FtsE, ATP-binding / NlpC/P60 domain profile. / Cell division protein FtsX / FtsX, extracellular domain / FtsX extracellular domain / Endopeptidase, NLPC/P60 domain / NlpC/P60 family / ABC transporter, lipoprotein release, LolD / ABC3 transporter permease protein domain / FtsX-like permease family / ABC transporter-like, conserved site / ABC transporters family signature. / Papain-like cysteine peptidase superfamily / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Cell division protein FtsX / Cell division ATP-binding protein FtsE / Probable endopeptidase MT2245
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsLi, J. / Xu, X. / Luo, M.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)A-0008412-00-00 Singapore
CitationJournal: Nat Commun / Year: 2023
Title: Regulation of the cell division hydrolase RipC by the FtsEX system in Mycobacterium tuberculosis.
Authors: Jianwei Li / Xin Xu / Jian Shi / Juan A Hermoso / Lok-To Sham / Min Luo /
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 ...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.
History
DepositionFeb 12, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Cell division ATP-binding protein FtsE
D: Cell division protein FtsX
C: Cell division protein FtsX
E: Probable endopeptidase MT2245
A: Cell division ATP-binding protein FtsE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,0437
Polymers157,0295
Non-polymers1,0142
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Cell division ATP-binding protein FtsE


Mass: 25766.697 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ftsE, Rv3102c, RVBD_3102c, LH57_16935, P425_03233
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O05779
#2: Protein Cell division protein FtsX /


Mass: 32851.355 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: ftsX
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A045GRS5
#3: Protein Probable endopeptidase MT2245 / NlpC/P60 family protein


Mass: 39792.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT2245
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P9WHU2, Hydrolases; Acting on peptide bonds (peptidases)
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: complex of FtsEX-RipC-ATP / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingAverage exposure time: 6.02 sec. / Electron dose: 38.837 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 111341 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0048888
ELECTRON MICROSCOPYf_angle_d1.00312098
ELECTRON MICROSCOPYf_dihedral_angle_d5.4971283
ELECTRON MICROSCOPYf_chiral_restr0.0561487
ELECTRON MICROSCOPYf_plane_restr0.0071554

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