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- EMDB-33300: Cryo-EM structure of PEIP-Bs_enolase complex -

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Basic information

Entry
Database: EMDB / ID: EMD-33300
TitleCryo-EM structure of PEIP-Bs_enolase complex
Map dataCryo-EM structure of PEIP-Bs_enolase complex
Sample
  • Complex: PEIP-Bs_enolase complex
    • Complex: Bs_enolase
      • Protein or peptide: Enolase
    • Complex: PEIP
      • Protein or peptide: Putative gene 60 protein
  • Ligand: MAGNESIUM ION
KeywordsEnolase 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 (strain 168) (bacteria) / Bacillus phage SP01 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsLi S / Zhang K
Funding support1 items
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, 2022-
Header (metadata) releaseJul 27, 2022-
Map releaseJul 27, 2022-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33300.png

Downloads & links

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Map

FileDownload / File: emd_33300.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of PEIP-Bs_enolase complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-5.965095 - 9.465401
Average (Standard dev.)0.008686091 (±0.22711702)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 209.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map-2

Fileemd_33300_half_map_1.map
Annotationhalf map-2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map-1

Fileemd_33300_half_map_2.map
Annotationhalf map-1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PEIP-Bs_enolase complex

EntireName: PEIP-Bs_enolase complex
Components
  • Complex: PEIP-Bs_enolase complex
    • Complex: Bs_enolase
      • Protein or peptide: Enolase
    • Complex: PEIP
      • Protein or peptide: Putative gene 60 protein
  • Ligand: MAGNESIUM ION

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Supramolecule #1: PEIP-Bs_enolase complex

SupramoleculeName: PEIP-Bs_enolase complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Molecular weightTheoretical: 100 KDa

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Supramolecule #2: Bs_enolase

SupramoleculeName: Bs_enolase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Bacillus subtilis (strain 168) (bacteria)

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Supramolecule #3: PEIP

SupramoleculeName: PEIP / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Bacillus phage SP01 (virus)

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Macromolecule #1: Enolase

MacromoleculeName: Enolase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: phosphopyruvate hydratase
Source (natural)Organism: Bacillus subtilis (strain 168) (bacteria)
Molecular weightTheoretical: 46.626148 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPYIVDVYAR EVLDSRGNPT VEVEVYTETG AFGRALVPSG ASTGEYEAVE LRDGDKDRYL GKGVLTAVNN VNEIIAPELL GFDVTEQNA IDQLLIELDG TENKGKLGAN AILGVSMACA RAAADFLQIP LYQYLGGFNS KTLPVPMMNI VNGGEHADNN V DIQEFMIM ...String:
MPYIVDVYAR EVLDSRGNPT VEVEVYTETG AFGRALVPSG ASTGEYEAVE LRDGDKDRYL GKGVLTAVNN VNEIIAPELL GFDVTEQNA IDQLLIELDG TENKGKLGAN AILGVSMACA RAAADFLQIP LYQYLGGFNS KTLPVPMMNI VNGGEHADNN V DIQEFMIM PVGAPNFREA LRMGAQIFHS LKSVLSAKGL NTAVGDEGGF APNLGSNEEA LQTIVEAIEK AGFKPGEEVK LA MDAASSE FYNKEDGKYH LSGEGVVKTS AEMVDWYEEL VSKYPIISIE DGLDENDWEG HKLLTERLGK KVQLVGDDLF VTN TKKLSE GIKNGVGNSI LIKVNQIGTL TETFDAIEMA KRAGYTAVIS HRSGETEDST IADIAVATNA GQIKTGAPSR TDRV AKYNQ LLRIEDQLAE TAQYHGINSF YNLNK

UniProtKB: Enolase

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Macromolecule #2: Putative gene 60 protein

MacromoleculeName: Putative gene 60 protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bacillus phage SP01 (virus)
Molecular weightTheoretical: 8.558438 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MLNQVEVLRE EYVEGYVVQM WRRNPSNAPV IEVFTEDNLE EGIIPEYVTA NDDTFDRIVD AVEFGYLEEL ELV

UniProtKB: Putative gene 60 protein

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 553242
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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