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- PDB-8g01: YES Complex - E. coli MraY, Protein E ID21, E. coli SlyD -

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Basic information

Entry
Database: PDB / ID: 8g01
TitleYES Complex - E. coli MraY, Protein E ID21, E. coli SlyD
Components
  • FKBP-type peptidyl-prolyl cis-trans isomerase SlyD
  • GPE
  • Phospho-N-acetylmuramoyl-pentapeptide-transferase
KeywordsTRANSFERASE/ISOMERASE / inhibitor / antibiotic / chaperone / membrane / bacteriophage / TRANSFERASE-ISOMERASE complex
Function / homology
Function and homology information


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
Phospho-N-acetylmuramoyl-pentapeptide-transferase / FKBP-type peptidyl-prolyl cis-trans isomerase SlyD / GPE
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
Escherichia phage ID21 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsOrta, A.K. / Clemons, W.M. / Riera, N.
Funding support United States, 2items
OrganizationGrant numberCountry
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
CitationJournal: 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.
History
DepositionJan 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / em_3d_fitting_list
Item: _em_3d_fitting_list.initial_refinement_model_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospho-N-acetylmuramoyl-pentapeptide-transferase
B: GPE
G: GPE
E: Phospho-N-acetylmuramoyl-pentapeptide-transferase
D: FKBP-type peptidyl-prolyl cis-trans isomerase SlyD
C: FKBP-type peptidyl-prolyl cis-trans isomerase SlyD


Theoretical massNumber of molelcules
Total (without water)132,1176
Polymers132,1176
Non-polymers00
Water00
1


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

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Components

#1: Protein Phospho-N-acetylmuramoyl-pentapeptide-transferase / UDP-MurNAc-pentapeptide phosphotransferase


Mass: 39909.539 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: mraY, murX, b0087, JW0085 / Production host: Escherichia coli K-12 (bacteria)
References: UniProt: P0A6W3, phospho-N-acetylmuramoyl-pentapeptide-transferase
#2: Protein GPE


Mass: 9489.507 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage ID21 (virus) / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q2LMB7
#3: Protein FKBP-type peptidyl-prolyl cis-trans isomerase SlyD / PPIase / Histidine-rich protein / Metallochaperone SlyD / Rotamase / Sensitivity to lysis protein D / WHP


Mass: 16659.486 Da / Num. of mol.: 2 / Fragment: UNP residues 1-154
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: slyD, b3349, JW3311 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A9K9, peptidylprolyl isomerase

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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
IDNameTypeDetailsEntity IDParent-IDSource
1YES complexCOMPLEXHexameric complex of E. coli MraY dimer bound to two molecules of Protein E (ID21), stabilized by E. coli SlyDall0MULTIPLE SOURCES
2Lysis Protein ECOMPLEXProtein E from ID21 phage#21RECOMBINANT
3Dimeric structure of MraYCOMPLEX#11RECOMBINANT
4SlyDCOMPLEXE. coli SlyD truncated at residue 154#31RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.14032 MDaNO
220.00865 MDaNO
330.03988 MDaNO
440.02086 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia phage ID21 (virus)338101
23Escherichia coli K-12 (bacteria)83333
34Escherichia coli K-12 (bacteria)83333
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli K-12 (bacteria)83333
23Escherichia coli K-12 (bacteria)83333
34Escherichia coli K-12 (bacteria)83333
Buffer solutionpH: 7.5 / Details: Supplemented with 2mM E. coli lipid extract
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMHEPESC8H18N2O4S1
275 mMSodium ChlorideNaCl1
35 %GlycerolC3H8O31
40.03 %n-Dodecyl-beta-maltosideC24H46O111
55 mM2-MercaptoethanolC2H6OS1
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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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: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2 sec. / Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 12070

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
EM software
IDNameVersionCategory
1cryoSPARCv3.2.0+210817particle selection
2DigitalMicrographimage acquisition
4cryoSPARCv3.2.0+210817CTF correction
7PHENIX1.20.1-4487model fitting
9cryoSPARCv3.2.0+210817initial Euler assignment
10cryoSPARCv3.2.0+210817final Euler assignment
11cryoSPARCv3.2.0+210817classification
12cryoSPARCv3.2.0+2108173D reconstruction
13PHENIX1.20.1-4487model refinement
14ISOLDE1.2.2model refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 11700795
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 122452 / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building

3D fitting-ID: 1 / Chain-ID: A / Pdb chain-ID: A / Source name: PDB / Type: experimental model

IDPDB-IDAccession codeChain residue rangeInitial refinement model-IDPdb chain residue range
14J72

4j72

4J721-36511-365
22K8I

2k8i

2K8I1-15421-154
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0029159
ELECTRON MICROSCOPYf_angle_d0.4212464
ELECTRON MICROSCOPYf_dihedral_angle_d3.9411231
ELECTRON MICROSCOPYf_chiral_restr0.0381458
ELECTRON MICROSCOPYf_plane_restr0.0031541

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