National Natural Science Foundation of China (NSFC)
31670749 and 31925024
China
Chinese Academy of Sciences
XDB08020302
China
Citation
Journal: Nat Commun / Year: 2021 Title: Phospholipid translocation captured in a bifunctional membrane protein MprF. Authors: Danfeng Song / Haizhan Jiao / Zhenfeng Liu / Abstract: As a large family of membrane proteins crucial for bacterial physiology and virulence, the Multiple Peptide Resistance Factors (MprFs) utilize two separate domains to synthesize and translocate ...As a large family of membrane proteins crucial for bacterial physiology and virulence, the Multiple Peptide Resistance Factors (MprFs) utilize two separate domains to synthesize and translocate aminoacyl phospholipids to the outer leaflets of bacterial membranes. The function of MprFs enables Staphylococcus aureus and other pathogenic bacteria to acquire resistance to daptomycin and cationic antimicrobial peptides. Here we present cryo-electron microscopy structures of MprF homodimer from Rhizobium tropici (RtMprF) at two different states in complex with lysyl-phosphatidylglycerol (LysPG). RtMprF contains a membrane-embedded lipid-flippase domain with two deep cavities opening toward the inner and outer leaflets of the membrane respectively. Intriguingly, a hook-shaped LysPG molecule is trapped inside the inner cavity with its head group bent toward the outer cavity which hosts a second phospholipid-binding site. Moreover, RtMprF exhibits multiple conformational states with the synthase domain adopting distinct positions relative to the flippase domain. Our results provide a detailed framework for understanding the mechanisms of MprF-mediated modification and translocation of phospholipids.
Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 30, 2013
Radiation
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Wavelength: 0.96 Å / Relative weight: 1
Reflection
Resolution: 1.998→50 Å / Num. obs: 57555 / % possible obs: 99.9 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 35.5
Reflection shell
Resolution: 1.998→2.07 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 8.3 / Num. unique obs: 5564 / % possible all: 99.7
-
Processing
Software
Name
Version
Classification
PHENIX
1.11.1_2575
refinement
PDB_EXTRACT
3.25
dataextraction
HKL-2000
datareduction
HKL-2000
datascaling
PHENIX
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.998→35.207 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.97 / Stereochemistry target values: ML
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.1984
2921
5.08 %
Random selection
Rwork
0.1683
54634
-
-
obs
0.1699
57555
99.78 %
-
Solvent computation
Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
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