4QIF

Crystal Structure of PduA with edge mutation K26A and pore mutation S40H


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9951 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Selective molecular transport through the protein shell of a bacterial microcompartment organelle.

Chowdhury, C.Chun, S.Pang, A.Sawaya, M.R.Sinha, S.Yeates, T.O.Bobik, T.A.

(2015) Proc.Natl.Acad.Sci.USA 112: 2990-2995

  • DOI: 10.1073/pnas.1423672112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterial microcompartments are widespread prokaryotic organelles that have important and diverse roles ranging from carbon fixation to enteric pathogenesis. Current models for microcompartment function propose that their outer protein shell is selec ...

    Bacterial microcompartments are widespread prokaryotic organelles that have important and diverse roles ranging from carbon fixation to enteric pathogenesis. Current models for microcompartment function propose that their outer protein shell is selectively permeable to small molecules, but whether a protein shell can mediate selective permeability and how this occurs are unresolved questions. Here, biochemical and physiological studies of structure-guided mutants are used to show that the hexameric PduA shell protein of the 1,2-propanediol utilization (Pdu) microcompartment forms a selectively permeable pore tailored for the influx of 1,2-propanediol (the substrate of the Pdu microcompartment) while restricting the efflux of propionaldehyde, a toxic intermediate of 1,2-propanediol catabolism. Crystal structures of various PduA mutants provide a foundation for interpreting the observed biochemical and phenotypic data in terms of molecular diffusion across the shell. Overall, these studies provide a basis for understanding a class of selectively permeable channels formed by nonmembrane proteins.


    Organizational Affiliation

    Molecular Biology Institute, UCLA-DOE Institute for Genomics and Proteomics, and Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095 bobik@iastate.edu yeates@mbi.ucla.edu.,Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011;,UCLA-DOE Institute for Genomics and Proteomics, and.,Molecular Biology Institute.,Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011; bobik@iastate.edu yeates@mbi.ucla.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Propanediol utilization protein PduA
A, B, C, D, E, F, G, H, I
102Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 2 
Gene Names: pduA
Find proteins for P0A1C7 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P0A1C7
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
TAR
Query on TAR

Download SDF File 
Download CCD File 
D, G
D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B, D, E, F, G, H
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PGO
Query on PGO

Download SDF File 
Download CCD File 
A, C, I
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9951 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.184 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 108.750α = 90.00
b = 108.750β = 90.00
c = 334.290γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHENIXrefinement
PHENIXphasing
SCALEPACKdata scaling
ADSCdata collection
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2015-02-25
    Type: Database references
  • Version 1.2: 2015-03-11
    Type: Database references
  • Version 1.3: 2015-03-25
    Type: Database references