+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33300 | |||||||||
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Title | Cryo-EM structure of PEIP-Bs_enolase complex | |||||||||
Map data | Cryo-EM structure of PEIP-Bs_enolase complex | |||||||||
Sample |
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Function / homology | Function and homology information phosphopyruvate hydratase / phosphopyruvate hydratase complex / phosphopyruvate hydratase activity / sporulation resulting in formation of a cellular spore / glycolytic process / magnesium ion binding / cell surface / extracellular region Similarity search - Function | |||||||||
Biological species | Bacillus subtilis (strain 168) (bacteria) / Bacillus phage SP01 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Li S / Zhang K | |||||||||
Funding support | 1 items
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Citation | Journal: 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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33300.map.gz | 32.9 MB | EMDB map data format | |
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Header (meta data) | emd-33300-v30.xml emd-33300.xml | 16.6 KB 16.6 KB | Display Display | EMDB header |
Images | emd_33300.png | 93.2 KB | ||
Others | emd_33300_half_map_1.map.gz emd_33300_half_map_2.map.gz | 59.3 MB 59.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33300 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33300 | HTTPS FTP |
-Related structure data
Related structure data | 7xmlMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33300.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM structure of PEIP-Bs_enolase complex | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.82 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map-2
File | emd_33300_half_map_1.map | ||||||||||||
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Annotation | half map-2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map-1
File | emd_33300_half_map_2.map | ||||||||||||
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Annotation | half map-1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : PEIP-Bs_enolase complex
Entire | Name: PEIP-Bs_enolase complex |
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Components |
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-Supramolecule #1: PEIP-Bs_enolase complex
Supramolecule | Name: PEIP-Bs_enolase complex / type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Molecular weight | Theoretical: 100 KDa |
-Supramolecule #2: Bs_enolase
Supramolecule | Name: Bs_enolase / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Bacillus subtilis (strain 168) (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Supramolecule #3: PEIP
Supramolecule | Name: PEIP / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Bacillus phage SP01 (virus) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Enolase
Macromolecule | Name: Enolase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: phosphopyruvate hydratase |
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Source (natural) | Organism: Bacillus subtilis (strain 168) (bacteria) |
Molecular weight | Theoretical: 46.626148 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #2: Putative gene 60 protein
Macromolecule | Name: Putative gene 60 protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus phage SP01 (virus) |
Molecular weight | Theoretical: 8.558438 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MLNQVEVLRE EYVEGYVVQM WRRNPSNAPV IEVFTEDNLE EGIIPEYVTA NDDTFDRIVD AVEFGYLEEL ELV |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
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Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Applied 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 |