3SYS

Improved crystal structure of Pseudomonas aeruginosa OccK1 (OpdK)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Substrate Specificity within a Family of Outer Membrane Carboxylate Channels.

Eren, E.Vijayaraghavan, J.Liu, J.Cheneke, B.R.Touw, D.S.Lepore, B.W.Indic, M.Movileanu, L.van den Berg, B.

(2012) Plos Biol. 10: e1001242-e1001242

  • DOI: 10.1371/journal.pbio.1001242
  • Primary Citation of Related Structures:  3SY7, 3SY9, 3SYB, 3SZD, 3SZV, 3T0S, 3T20, 3T24

  • PubMed Abstract: 
  • Many Gram-negative bacteria, including human pathogens such as Pseudomonas aeruginosa, do not have large-channel porins. This results in an outer membrane (OM) that is highly impermeable to small polar molecules, making the bacteria intrinsically res ...

    Many Gram-negative bacteria, including human pathogens such as Pseudomonas aeruginosa, do not have large-channel porins. This results in an outer membrane (OM) that is highly impermeable to small polar molecules, making the bacteria intrinsically resistant towards many antibiotics. In such microorganisms, the majority of small molecules are taken up by members of the OprD outer membrane protein family. Here we show that OprD channels require a carboxyl group in the substrate for efficient transport, and based on this we have renamed the family Occ, for outer membrane carboxylate channels. We further show that Occ channels can be divided into two subfamilies, based on their very different substrate specificities. Our results rationalize how certain bacteria can efficiently take up a variety of substrates under nutrient-poor conditions without compromising membrane permeability. In addition, they explain how channel inactivation in response to antibiotics can cause resistance but does not lead to decreased fitness.


    Organizational Affiliation

    University of Massachusetts Medical School, Program in Molecular Medicine, Worcester, Massachusetts, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vanillate porin OpdK
A, B
398Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228)Gene Names: opdK
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Outer Membrane Carboxylate Channels (Occ)
Protein: 
OccK1 (OpdK) benzoate channel
Find proteins for Q9HUR5 (Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228))
Go to UniProtKB:  Q9HUR5
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C8E
Query on C8E

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

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
VNL
Query on VNL

Download SDF File 
Download CCD File 
A, B
4-HYDROXY-3-METHOXYBENZOATE
vanillate
C8 H7 O4
WKOLLVMJNQIZCI-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 82.142α = 90.00
b = 96.840β = 90.00
c = 121.557γ = 90.00
Software Package:
Software NamePurpose
CBASSdata collection
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-08
    Type: Initial release