4PPD

PduA K26A, crystal form 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Alanine scanning mutagenesis identifies an asparagine-arginine-lysine triad essential to assembly of the shell of the pdu microcompartment.

Sinha, S.Cheng, S.Sung, Y.W.McNamara, D.E.Sawaya, M.R.Yeates, T.O.Bobik, T.A.

(2014) J.Mol.Biol. 426: 2328-2345

  • DOI: 10.1016/j.jmb.2014.04.012
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterial microcompartments (MCPs) are the simplest organelles known. They function to enhance metabolic pathways by confining several related enzymes inside an all-protein envelope called the shell. In this study, we investigated the factors that go ...

    Bacterial microcompartments (MCPs) are the simplest organelles known. They function to enhance metabolic pathways by confining several related enzymes inside an all-protein envelope called the shell. In this study, we investigated the factors that govern MCP assembly by performing scanning mutagenesis on the surface residues of PduA, a major shell protein of the MCP used for 1,2-propanediol degradation. Biochemical, genetic, and structural analysis of 20 mutants allowed us to determine that PduA K26, N29, and R79 are crucial residues that stabilize the shell of the 1,2-propanediol MCP. In addition, we identify two PduA mutants (K37A and K55A) that impair MCP function most likely by altering the permeability of its protein shell. These are the first studies to examine the phenotypic effects of shell protein structural mutations in an MCP system. The findings reported here may be applicable to engineering protein containers with improved stability for biotechnology applications.


    Organizational Affiliation

    Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Propanediol utilization protein PduA
A, B, C, D, E, F, G
100Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 1 
Gene Names: pduA
Find proteins for P0A1C7 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  P0A1C7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
A, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.195 
  • Space Group: F 2 3
Unit Cell:
Length (Å)Angle (°)
a = 235.340α = 90.00
b = 235.340β = 90.00
c = 235.340γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHENIXrefinement
PHASERphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-05-14
    Type: Initial release
  • Version 1.1: 2014-06-04
    Type: Database references