3SY9

Crystal structure of Pseudomonas aeruginosa OccD2 (OpdC)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.1 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:  
    3T20, 3T0S, 3T24, 3SY7, 3SYS, 3SYB, 3SY9, 3SZV, 3SZD

  • 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 resista ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histidine porin OpdC A, B, C, D430Pseudomonas aeruginosaMutation(s): 0 
Gene Names: opdC, PA0162
Membrane protein
Mpstruc		Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL		Sub Group: 
Outer Membrane Carboxylate Channels (Occ)		Protein: 
OccD2 (OpdC) basic amino acid uptake channel
Find proteins for Q9I6X0 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9I6X0 
Go to UniProtKB:  Q9I6X0
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.353α = 77.67
b = 102.828β = 62.57
c = 101.696γ = 62.95
Software Package:
Software NamePurpose
CBASSdata collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-02-08
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary