Crystal structure of the drug-discharge outer membrane protein, OprM

Experimental Data Snapshot

  • Resolution: 2.56 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.255 

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Crystal structure of the drug discharge outer membrane protein, OprM, of Pseudomonas aeruginosa: dual modes of membrane anchoring and occluded cavity end

Akama, H.Kanemaki, M.Yoshimura, M.Tsukihara, T.Kashiwagi, T.Yoneyama, H.Narita, S.Nakagawa, A.Nakae, T.

(2004) J Biol Chem 279: 52816-52819

  • DOI: https://doi.org/10.1074/jbc.C400445200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The OprM lipoprotein of Pseudomonas aeruginosa is a member of the MexAB-OprM xenobiotic-antibiotic transporter subunits that is assumed to serve as the drug discharge duct across the outer membrane. The channel structure must differ from that of the porin-type open pore because the protein facilitates the exit of antibiotics but not the entry. For better understanding of the structure-function linkage of this important pump subunit, we studied the x-ray crystallographic structure of OprM at the 2.56-angstroms resolution. The overall structure exhibited trimeric assembly of the OprM monomer that consisted mainly of two domains: the membrane-anchoring beta-barrel and the cavity-forming alpha-barrel. OprM anchors the outer membrane by two modes of membrane insertions. One is via the covalently attached NH(2)-terminal fatty acids and the other is the beta-barrel structure consensus on the outer membrane-spanning proteins. The beta-barrel had a pore opening with a diameter of about 6-8 angstroms, which is not large enough to accommodate the exit of any antibiotics. The periplasmic alpha-barrel was about 100 angstroms long formed mainly by a bundle of alpha-helices that formed a solvent-filled cavity of about 25,000 angstroms(3). The proximal end of the cavity was tightly sealed, thereby not permitting the entry of any molecule. The result of this structure was that the resting state of OprM had a small outer membrane pore and a tightly closed periplasmic end, which sounds plausible because the protein should not allow free access of antibiotics. However, these observations raised another unsolved problem about the mechanism of opening of the OprM cavity ends. The crystal structure offers possible mechanisms of pore opening and pump assembly.

  • Organizational Affiliation

    Department of Molecular Life Science, Tokai University School of Medicine, Isehara 259-1193, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein oprM
A, B
474Pseudomonas aeruginosaMutation(s): 0 
Gene Names: oprM
Membrane Entity: Yes 
Find proteins for Q51487 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q51487 
Go to UniProtKB:  Q51487
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ51487
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.56 Å
  • R-Value Free: 0.308 
  • R-Value Work: 0.252 
  • R-Value Observed: 0.255 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.43α = 90
b = 85.43β = 90
c = 1044.3γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Derived calculations, Refinement description, Version format compliance
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references