4GEY

High pH structure of Pseudomonas putida OprB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


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: 10.1074/jbc.M112.408518
  • Primary Citation of Related Structures:  

  • 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 char ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Porin B
A
436Pseudomonas putida (strain ATCC 700007 / DSM 6899 / BCRC 17059 / F1)Mutation(s): 2 
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Beta-Barrel Membrane Proteins: Porins and Relatives
Protein: 
OprB carbohydrate-specific transporter at high pH
Find proteins for A5VZA8 (Pseudomonas putida (strain ATCC 700007 / DSM 6899 / BCRC 17059 / F1))
Go to UniProtKB:  A5VZA8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
DMU
Query on DMU

Download SDF File 
Download CCD File 
A
DECYL-BETA-D-MALTOPYRANOSIDE
DECYLMALTOSIDE
C22 H42 O11
WOQQAWHSKSSAGF-WXFJLFHKSA-N
 Ligand Interaction
C8E
Query on C8E

Download SDF File 
Download CCD File 
A
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
 Ligand Interaction
BGC
Query on BGC

Download SDF File 
Download CCD File 
A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.188 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 88.343α = 90.00
b = 88.343β = 90.00
c = 177.706γ = 120.00
Software Package:
Software NamePurpose
CBASSdata collection
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction
PHENIXrefinement
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-08-02 
  • Released Date: 2012-10-24 
  • Deposition Author(s): van den Berg, B.

Revision History 

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