3N79

PduT C38S Mutant from Salmonella enterica Typhimurium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural Insight into the Mechanisms of Transport across the Salmonella enterica Pdu Microcompartment Shell.

Crowley, C.S.Cascio, D.Sawaya, M.R.Kopstein, J.S.Bobik, T.A.Yeates, T.O.

(2010) J Biol Chem 285: 37838-37846

  • DOI: https://doi.org/10.1074/jbc.M110.160580
  • Primary Citation of Related Structures:  
    3N79, 3NGK

  • PubMed Abstract: 

    Bacterial microcompartments are a functionally diverse group of proteinaceous organelles that confine specific reaction pathways in the cell within a thin protein-based shell. The propanediol utilizing (Pdu) microcompartment contains the reactions for metabolizing 1,2-propanediol in certain enteric bacteria, including Salmonella. The Pdu shell is assembled from a few thousand protein subunits of several different types. Here we report the crystal structures of two key shell proteins, PduA and PduT. The crystal structures offer insights into the mechanisms of Pdu microcompartment assembly and molecular transport across the shell. PduA forms a symmetric homohexamer whose central pore appears tailored for facilitating transport of the 1,2-propanediol substrate. PduT is a novel, tandem domain shell protein that assembles as a pseudohexameric homotrimer. Its structure reveals an unexpected site for binding an [Fe-S] cluster at the center of the PduT pore. The location of a metal redox cofactor in the pore of a shell protein suggests a novel mechanism for either transferring redox equivalents across the shell or for regenerating luminal [Fe-S] clusters.


  • Organizational Affiliation

    Molecular Biology Institute, Iowa State University, Ames, Iowa 50011, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PduT192Salmonella enterica subsp. enterica serovar TyphimuriumMutation(s): 1 
Gene Names: pduTSTM2054
UniProt
Find proteins for Q9XDM8 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Explore Q9XDM8 
Go to UniProtKB:  Q9XDM8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9XDM8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.68α = 90
b = 67.68β = 90
c = 61.62γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
SHELXphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SHELXDphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references, Derived calculations