4GF4

Low pH structure of Pseudomonas putida OprB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.220 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural basis for outer membrane sugar uptake in pseudomonads.

van den Berg, B.

(2012) J Biol Chem 287: 41044-41052

  • DOI: https://doi.org/10.1074/jbc.M112.408518
  • Primary Citation of Related Structures:  
    4GF4

  • PubMed Abstract: 

    Substrate-specific outer membrane channels of gram-negative bacteria mediate uptake of many small molecules, including carbohydrates. The mechanism of sugar uptake by enterobacterial channels, such as Escherichia coli LamB (maltoporin), has been characterized in great detail. In pseudomonads and related organisms, sugar uptake is not mediated by LamB but by OprB channels. Beyond the notion that OprB channels seem to prefer monosaccharides as substrates, very little is known about OprB-mediated sugar uptake. Here I report the X-ray crystal structure of an OprB channel from Pseudomonas putida F1. The structure shows that OprB forms a monomeric, 16-stranded β-barrel with a constriction formed by extracellular loops L2 and L3. The side chains of two highly conserved arginine residues (Arg(83) and Arg(110)) and a conserved glutamate (Glu(106)) line the channel constriction and interact with a bound glucose molecule. Liposome swelling uptake assays show a strong preference for monosaccharide transport over disaccharides. Moreover, substrates with a net negative charge are disfavored by the channel, probably due to the negatively charged character of the constriction. The architecture of the eyelet and the absence of a greasy slide provide an explanation for the observed specificity of OprB for monosaccharides rather than the oligosaccharides preferred by LamB and related enterobacterial channels.


  • Organizational Affiliation

    Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA. bert.vandenberg@umassmed.edu


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Porin B436Pseudomonas putida BIRD-1Mutation(s): 4 
Gene Names: PPUBIRD1_1069
Membrane Entity: Yes 
UniProt
Find proteins for A5VZA8 (Pseudomonas putida (strain ATCC 700007 / DSM 6899 / BCRC 17059 / F1))
Explore A5VZA8 
Go to UniProtKB:  A5VZA8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5VZA8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.220 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.037α = 90
b = 122.592β = 90
c = 135.581γ = 90
Software Package:
Software NamePurpose
CBASSdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-24
    Type: Initial release
  • Version 1.1: 2012-11-07
    Changes: Database references
  • Version 1.2: 2013-01-02
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description