+Open data
-Basic information
Entry | Database: PDB / ID: 8tlu | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | E. coli MraY mutant-T23P | |||||||||
Components | Phospho-N-acetylmuramoyl-pentapeptide-transferase | |||||||||
Keywords | MEMBRANE PROTEIN / peptidoglycan / phosphotransferase | |||||||||
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 / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / membrane ...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 / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Orta, A.K. / Li, Y.E. / Clemons, W.M. | |||||||||
Funding support | United States, 2items
| |||||||||
Citation | Journal: Nat Microbiol / Year: 2024 Title: Synthesis of lipid-linked precursors of the bacterial cell wall is governed by a feedback control mechanism in Pseudomonas aeruginosa. Authors: Lindsey S Marmont / Anna K Orta / Becca W A Baileeves / David Sychantha / Ana Fernández-Galliano / Yancheng E Li / Neil G Greene / Robin A Corey / Phillip J Stansfeld / William M Clemons / ...Authors: Lindsey S Marmont / Anna K Orta / Becca W A Baileeves / David Sychantha / Ana Fernández-Galliano / Yancheng E Li / Neil G Greene / Robin A Corey / Phillip J Stansfeld / William M Clemons / Thomas G Bernhardt / Abstract: Many bacterial surface glycans such as the peptidoglycan (PG) cell wall are built from monomeric units linked to a polyprenyl lipid carrier. How this limiting carrier is distributed among competing ...Many bacterial surface glycans such as the peptidoglycan (PG) cell wall are built from monomeric units linked to a polyprenyl lipid carrier. How this limiting carrier is distributed among competing pathways has remained unclear. Here we describe the isolation of hyperactive variants of Pseudomonas aeruginosa MraY, the enzyme that forms the first lipid-linked PG precursor. These variants result in the elevated production of the final PG precursor lipid II in cells and are hyperactive in vitro. The activated MraY variants have substitutions that map to a cavity on the extracellular side of the dimer interface, far from the active site. Our structural and molecular dynamics results suggest that this cavity is a binding site for externalized lipid II. Overall, our results support a model in which excess externalized lipid II allosterically inhibits MraY, providing a feedback mechanism that prevents the sequestration of lipid carrier in the PG biogenesis pathway. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8tlu.cif.gz | 235.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8tlu.ent.gz | 192.1 KB | Display | PDB format |
PDBx/mmJSON format | 8tlu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/8tlu ftp://data.pdbj.org/pub/pdb/validation_reports/tl/8tlu | HTTPS FTP |
---|
-Related structure data
Related structure data | 41373MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 39905.551 Da / Num. of mol.: 2 / Mutation: T23P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: mraY / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P0A6W3 |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: E. coli MraY T23P dimer / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT |
---|---|
Molecular weight | Value: 0.039875 MDa / Experimental value: NO |
Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Source (recombinant) | Organism: Escherichia coli K-12 (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: MraY was pulled down using the YES complex. |
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 500 nm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 |
-Processing
EM software |
| ||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 287765 / Num. of class averages: 1 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 8G01 Pdb chain-ID: A / Accession code: 8G01 / Chain residue range: 1-360 / Pdb chain residue range: 1-360 / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|