9W50 | pdb_00009w50

MprF from Pseudomonas aeruginosa mutant- H386C/F389C in nanodisc, C2 symmetry


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Literature

Cryo-EM structures of multiple-peptide resistance factor (MprF) from Pseudomonas aeruginosa.

Jha, S.Vinothkumar, K.R.

(2026) FEBS J 

  • DOI: https://doi.org/10.1111/febs.70519
  • Primary Citation Related Structures: 
    9J8Q, 9J8R, 9J8S, 9W50, 9W51

  • PubMed Abstract: 

    Aminoacylation of the lipid head group in many bacteria is carried out by bi-functional enzymes called MprF, which encode a soluble synthase domain that typically transfers lysine or alanine from a tRNA to lipid head groups. The modified lipid is subsequently translocated across the leaflets by a transmembrane domain. This modification of lipids probably evolved to adapt to the environment where the microbes reside. Here, we describe the cryo-EM structures of MprF enzyme from Pseudomonas aeruginosa, revealing a dimeric enzyme with a distinct architecture when compared with the homologous Rhizobium enzymes, and validate this arrangement with biochemical analyses. The cryo-EM maps and the models in detergent micelle and nanodisc reveal a conformational change of the terminal helix of the synthase domain, highlighting the dynamic elements in the enzyme that might facilitate catalysis. Several lipid-like densities are observed in the cryo-EM maps, which might indicate the path taken by the lipids, coupling the function of the two domains. The structures allow postulation of the binding modes of tRNA and lipid transport, and suggest that the mobile secondary structural elements in the synthase domain might play a mechanistic role in these functions.


  • Organizational Affiliation
    • National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, India.

Macromolecule Content 

  • Total Structure Weight: 199.51 kDa 
  • Atom Count: 12,502 
  • Modeled Residue Count: 1,604 
  • Deposited Residue Count: 1,806 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Phosphatidylglycerol lysyltransferase
A, B
903Pseudomonas aeruginosa PAO1Mutation(s): 2 
Gene Names: PA0920
EC: 2.3.2.3
UniProt
Find proteins for Q9I537 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I537 
Go to UniProtKB:  Q9I537
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9I537
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.5.3
MODEL REFINEMENTPHENIX1.21.2-5419
MODEL REFINEMENTREFMAC5.8.0430

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentIndiaDepartment of Atomic Energy, Government of India, RTI 4006
Department of Biotechnology (DBT, India)IndiaDBT/PR12422/MED/31/287/2014

Revision History  (Full details and data files)

  • Version 1.0: 2026-06-03
    Type: Initial release