phospho-N-acetylmuramoyl-pentapeptide-transferase / UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine:undecaprenyl-phosphate transferase activity / phospho-N-acetylmuramoyl-pentapeptide-transferase activity / cell wall macromolecule biosynthetic process / modulation by virus of host cellular process / enzyme inhibitor activity / protein maturation by protein folding / cobalt ion binding / nickel cation binding / protein maturation ...phospho-N-acetylmuramoyl-pentapeptide-transferase / UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine:undecaprenyl-phosphate transferase activity / phospho-N-acetylmuramoyl-pentapeptide-transferase activity / cell wall macromolecule biosynthetic process / modulation by virus of host cellular process / enzyme inhibitor activity / protein maturation by protein folding / cobalt ion binding / nickel cation binding / protein maturation / peptidoglycan biosynthetic process / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / cell wall organization / unfolded protein binding / regulation of cell shape / response to heat / protein refolding / killing of cells of another organism / protein stabilization / cell cycle / copper ion binding / cell division / zinc ion binding / membrane / metal ion binding / plasma membrane / cytosol Similarity search - Function
Microvirus lysis protein (E) / Microvirus lysis protein (E), C terminus / : / Phospho-N-acetylmuramoyl-pentapeptide transferase / Phospho-N-acetylmuramoyl-pentapeptide transferase, conserved site / Phospho-N-acetylmuramoyl-pentapeptide-transferase signature 1 / MraY family signature 1. / MraY family signature 2. / Glycosyl transferase, family 4 / Glycosyl transferase family 4 ...Microvirus lysis protein (E) / Microvirus lysis protein (E), C terminus / : / Phospho-N-acetylmuramoyl-pentapeptide transferase / Phospho-N-acetylmuramoyl-pentapeptide transferase, conserved site / Phospho-N-acetylmuramoyl-pentapeptide-transferase signature 1 / MraY family signature 1. / MraY family signature 2. / Glycosyl transferase, family 4 / Glycosyl transferase family 4 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily Similarity search - Domain/homology
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
GM114611
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
GM105385
United States
Citation
Journal: Science / Year: 2023 Title: The mechanism of the phage-encoded protein antibiotic from ΦX174. Authors: Anna K Orta / Nadia Riera / Yancheng E Li / Shiho Tanaka / Hyun Gi Yun / Lada Klaic / William M Clemons / Abstract: The historically important phage ΦX174 kills its host bacteria by encoding a 91-residue protein antibiotic called protein E. Using single-particle electron cryo-microscopy, we demonstrate that ...The historically important phage ΦX174 kills its host bacteria by encoding a 91-residue protein antibiotic called protein E. Using single-particle electron cryo-microscopy, we demonstrate that protein E bridges two bacterial proteins to form the transmembrane YES complex [MraY, protein E, sensitivity to lysis D (SlyD)]. Protein E inhibits peptidoglycan biosynthesis by obstructing the MraY active site leading to loss of lipid I production. We experimentally validate this result for two different viral species, providing a clear model for bacterial lysis and unifying previous experimental data. Additionally, we characterize the MraY structure-revealing features of this essential enzyme-and the structure of the chaperone SlyD bound to a protein. Our structures provide insights into the mechanism of phage-mediated lysis and for structure-based design of phage therapeutics.
Protein or peptide: Phospho-N-acetylmuramoyl-pentapeptide-transferase
Complex: SlyD
Protein or peptide: FKBP-type peptidyl-prolyl cis-trans isomerase SlyD
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Supramolecule #1: YES complex
Supramolecule
Name: YES complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Hexameric complex of E. coli MraY dimer bound to two molecules of Protein E (ID21), stabilized by E. coli SlyD
Molecular weight
Theoretical: 140.32 KDa
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Supramolecule #2: Lysis Protein E
Supramolecule
Name: Lysis Protein E / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #2 / Details: Protein E from ID21 phage
Details: Supplemented with 2mM E. coli lipid extract
Grid
Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
Vitrification
Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
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Electron microscopy
Microscope
FEI TITAN KRIOS
Image recording
Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 12070 / Average exposure time: 2.0 sec. / Average electron dose: 60.0 e/Å2
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Number classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. v3.2.0+210817) / Number images used: 122452
Initial angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.2.0+210817)
Final angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v3.2.0+210817)
Final 3D classification
Number classes: 4 / Avg.num./class: 69806 / Software - Name: cryoSPARC (ver. v3.2.0+210817) Details: Two classes had about 100,000+ particles, one had about 37,000 and the final class about 5,000
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