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- PDB-8y3x: Cell divisome sPG hydrolysis machinery FtsEX-EnvC -

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Basic information

Entry
Database: PDB / ID: 8y3x
TitleCell divisome sPG hydrolysis machinery FtsEX-EnvC
Components
  • Cell division ATP-binding protein FtsE
  • Cell division protein FtsX
  • Murein hydrolase activator EnvC
KeywordsMEMBRANE PROTEIN / CELL DIVISION
Function / homology
Function and homology information


division septum / divisome complex / peptidoglycan-based cell wall biogenesis / Gram-negative-bacterium-type cell wall / septum digestion after cytokinesis / peptidoglycan turnover / plasma membrane protein complex / division septum assembly / FtsZ-dependent cytokinesis / extrinsic component of membrane ...division septum / divisome complex / peptidoglycan-based cell wall biogenesis / Gram-negative-bacterium-type cell wall / septum digestion after cytokinesis / peptidoglycan turnover / plasma membrane protein complex / division septum assembly / FtsZ-dependent cytokinesis / extrinsic component of membrane / cell division site / ATPase complex / positive regulation of cell division / transmembrane transporter activity / response to radiation / transmembrane transport / metalloendopeptidase activity / outer membrane-bounded periplasmic space / periplasmic space / hydrolase activity / response to xenobiotic stimulus / cell division / response to antibiotic / ATP hydrolysis activity / ATP binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / Cell division protein FtsE, ATP-binding / Cell division protein FtsX / FtsX, extracellular domain / FtsX extracellular domain / : / ABC transporter, lipoprotein release, LolD / Peptidase M23 / Peptidase family M23 / ABC3 transporter permease protein domain ...: / Cell division protein FtsE, ATP-binding / Cell division protein FtsX / FtsX, extracellular domain / FtsX extracellular domain / : / ABC transporter, lipoprotein release, LolD / Peptidase M23 / Peptidase family M23 / ABC3 transporter permease protein domain / Duplicated hybrid motif / FtsX-like permease family / ABC transporter-like, conserved site / ABC transporters family signature. / 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 ATP-binding protein FtsE / Cell division protein FtsX / Murein hydrolase activator EnvC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsZhang, Z. / Dong, H. / Chen, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31800052 China
CitationJournal: PLoS Biol / Year: 2024
Title: Structure and activity of the septal peptidoglycan hydrolysis machinery crucial for bacterial cell division.
Authors: Yatian Chen / Jiayue Gu / Biao Yang / Lili Yang / Jie Pang / Qinghua Luo / Yirong Li / Danyang Li / Zixin Deng / Changjiang Dong / Haohao Dong / Zhengyu Zhang /
Abstract: The peptidoglycan (PG) layer is a critical component of the bacterial cell wall and serves as an important target for antibiotics in both gram-negative and gram-positive bacteria. The hydrolysis of ...The peptidoglycan (PG) layer is a critical component of the bacterial cell wall and serves as an important target for antibiotics in both gram-negative and gram-positive bacteria. The hydrolysis of septal PG (sPG) is a crucial step of bacterial cell division, facilitated by FtsEX through an amidase activation system. In this study, we present the cryo-EM structures of Escherichia coli FtsEX and FtsEX-EnvC in the ATP-bound state at resolutions of 3.05 Å and 3.11 Å, respectively. Our PG degradation assays in E. coli reveal that the ATP-bound conformation of FtsEX activates sPG hydrolysis of EnvC-AmiB, whereas EnvC-AmiB alone exhibits autoinhibition. Structural analyses indicate that ATP binding induces conformational changes in FtsEX-EnvC, leading to significant differences from the apo state. Furthermore, PG degradation assays of AmiB mutants confirm that the regulation of AmiB by FtsEX-EnvC is achieved through the interaction between EnvC-AmiB. These findings not only provide structural insight into the mechanism of sPG hydrolysis and bacterial cell division, but also have implications for the development of novel therapeutics targeting drug-resistant bacteria.
History
DepositionJan 29, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: 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
A: Cell division ATP-binding protein FtsE
B: Cell division ATP-binding protein FtsE
C: Cell division protein FtsX
D: Cell division protein FtsX
E: Murein hydrolase activator EnvC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,7947
Polymers172,7795
Non-polymers1,0142
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Cell division ATP-binding protein FtsE


Mass: 24475.295 Da / Num. of mol.: 2 / Mutation: E163Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ftsE, b3463, JW3428 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A9R7
#2: Protein Cell division protein FtsX


Mass: 38583.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ftsX, ftsS, b3462, JW3427 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AC30
#3: Protein Murein hydrolase activator EnvC / Septal ring factor


Mass: 46661.617 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: envC, yibP, b3613, JW5646 / Production host: Escherichia coli (E. coli) / References: UniProt: P37690
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
Has ligand of interestY

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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: FtsEX-EnvC / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Escherichia coli (E. coli)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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: OTHER
Electron lensMode: OTHER / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4039317 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0069221
ELECTRON MICROSCOPYf_angle_d0.65812631
ELECTRON MICROSCOPYf_dihedral_angle_d5.6851521
ELECTRON MICROSCOPYf_chiral_restr0.0441568
ELECTRON MICROSCOPYf_plane_restr0.0051672

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