4QIF

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 

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 U S A 112: 2990-2995

  • DOI: 10.1073/pnas.1423672112
  • Primary Citation of Related Structures:  
    4QIF, 4QIG, 4RBT, 4RBU, 4RBV

  • 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 selectively permeable to small molecules, but whether a protein shell can mediate selective permeability and how this occurs are unresolved questions ...

    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

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Propanediol utilization protein PduA
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I
102Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Mutation(s): 2 
Gene Names: pduASTM2038
UniProt
Find proteins for P0A1C7 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore P0A1C7 
Go to UniProtKB:  P0A1C7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TAR
Query on TAR

Download Ideal Coordinates CCD File 
EA [auth G], U [auth D], V [auth D]D(-)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-LWMBPPNESA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth E] , BA [auth F] , GA [auth G] , IA [auth H] , JA [auth H] , K [auth A] , L [auth A] , M [auth A] , 
AA [auth E],  BA [auth F],  GA [auth G],  IA [auth H],  JA [auth H],  K [auth A],  L [auth A],  M [auth A],  N [auth A],  Q [auth B],  R [auth B],  S [auth C],  X [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth F], DA [auth F], FA [auth G], HA [auth H], P [auth B], W [auth D], Y [auth E], Z [auth E]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PGO
Query on PGO

Download Ideal Coordinates CCD File 
J [auth A], KA [auth I], T [auth C]S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
O [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.187 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.75α = 90
b = 108.75β = 90
c = 334.29γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXmodel building
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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