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- PDB-7xml: Cryo-EM structure of PEIP-Bs_enolase complex -

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Basic information

Entry
Database: PDB / ID: 7xml
TitleCryo-EM structure of PEIP-Bs_enolase complex
Components
  • Enolase
  • Putative gene 60 protein
KeywordsLYASE/LYASE INHIBITOR / Enolase inhibitor / Glycolysis / Bacteriophage / ANTIMICROBIAL PROTEIN / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / sporulation resulting in formation of a cellular spore / glycolytic process / cell surface / magnesium ion binding / extracellular region
Similarity search - Function
Enolase / Enolase, conserved site / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase signature. / Enolase, C-terminal TIM barrel domain / Enolase, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily
Similarity search - Domain/homology
Putative gene 60 protein / Enolase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
Bacillus phage SP01 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLi, S. / Zhang, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cell Rep / Year: 2022
Title: Bacteriophage protein PEIP is a potent Bacillus subtilis enolase inhibitor.
Authors: Kaining Zhang / Shanshan Li / Yawen Wang / Zhihao Wang / Nancy Mulvenna / Hang Yang / Peipei Zhang / Huan Chen / Yan Li / Hongliang Wang / Yongxiang Gao / Sivaramesh Wigneshweraraj / Steve ...Authors: Kaining Zhang / Shanshan Li / Yawen Wang / Zhihao Wang / Nancy Mulvenna / Hang Yang / Peipei Zhang / Huan Chen / Yan Li / Hongliang Wang / Yongxiang Gao / Sivaramesh Wigneshweraraj / Steve Matthews / Kaiming Zhang / Bing Liu /
Abstract: Enolase is a highly conserved enzyme that presents in all organisms capable of glycolysis or fermentation. Its immediate product phosphoenolpyruvate is essential for other important processes like ...Enolase is a highly conserved enzyme that presents in all organisms capable of glycolysis or fermentation. Its immediate product phosphoenolpyruvate is essential for other important processes like peptidoglycan synthesis and the phosphotransferase system in bacteria. Therefore, enolase inhibitors are of great interest. Here, we report that Gp60, a phage-encoded enolase inhibitor protein (PEIP) of bacteriophage SPO1 for Bacillus subtilis, is an enolase inhibitor. PEIP-expressing bacteria exhibit growth attenuation, thinner cell walls, and safranin color in Gram staining owing to impaired peptidoglycan synthesis. We solve the structure of PEIP-enolase tetramer and show that PEIP disassembles enolase by disrupting the basic dimer unit. The structure reveals that PEIP does not compete for substrate binding but induces a cascade of conformational changes that limit accessibility to the enolase catalytic site. This phage-inspired disassembly of enolase represents an alternative strategy for the development of anti-microbial drugs.
History
DepositionApr 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enolase
C: Putative gene 60 protein
B: Enolase
D: Putative gene 60 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,4186
Polymers110,3694
Non-polymers492
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Enolase / 2-phospho-D-glycerate hydro-lyase / 2-phosphoglycerate dehydratase


Mass: 46626.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: eno, BSU33900 / Production host: Escherichia coli (E. coli) / References: UniProt: P37869, phosphopyruvate hydratase
#2: Protein Putative gene 60 protein / PEIP


Mass: 8558.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage SP01 (virus) / Gene: 60 / Production host: Escherichia coli (E. coli) / References: UniProt: O48414
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
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

Component
IDNameTypeEntity IDParent-IDSource
1PEIP-Bs_enolase complexCOMPLEX#1-#20RECOMBINANT
2Bs_enolaseCOMPLEX#11RECOMBINANT
3PEIPCOMPLEX#21RECOMBINANT
Molecular weightValue: 0.1 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Bacillus subtilis (strain 168) (bacteria)224308
23Bacillus phage SP01 (virus)10685
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli (E. coli)562
23Escherichia coli (E. coli)562
Buffer solutionpH: 6.5
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2300 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
CTF correctionType: NONE
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 553242 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0097748
ELECTRON MICROSCOPYf_angle_d0.89410504
ELECTRON MICROSCOPYf_dihedral_angle_d5.8164652
ELECTRON MICROSCOPYf_chiral_restr0.0591188
ELECTRON MICROSCOPYf_plane_restr0.0061396

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