3BN0

The ribosomal protein S16 from Aquifex aeolicus


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.241 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Extreme temperature tolerance of a hyperthermophilic protein coupled to residual structure in the unfolded state

Wallgren, M.Aden, J.Pylypenko, O.Mikaelsson, T.Johansson, L.B.-A.Rak, A.Wolf-Watz, M.

(2008) J Mol Biol 379: 845-858

  • DOI: 10.1016/j.jmb.2008.04.007
  • Primary Citation of Related Structures:  
    3BN0

  • PubMed Abstract: 
  • Understanding the mechanisms that dictate protein stability is of large relevance, for instance, to enable design of temperature-tolerant enzymes with high enzymatic activity over a broad temperature interval. In an effort to identify such mechanisms ...

    Understanding the mechanisms that dictate protein stability is of large relevance, for instance, to enable design of temperature-tolerant enzymes with high enzymatic activity over a broad temperature interval. In an effort to identify such mechanisms, we have performed a detailed comparative study of the folding thermodynamics and kinetics of the ribosomal protein S16 isolated from a mesophilic (S16(meso)) and hyperthermophilic (S16(thermo)) bacterium by using a variety of biophysical methods. As basis for the study, the 2.0 A X-ray structure of S16(thermo) was solved using single wavelength anomalous dispersion phasing. Thermal unfolding experiments yielded midpoints of 59 and 111 degrees C with associated changes in heat capacity upon unfolding (DeltaC(p)(0)) of 6.4 and 3.3 kJ mol(-1) K(-1), respectively. A strong linear correlation between DeltaC(p)(0) and melting temperature (T(m)) was observed for the wild-type proteins and mutated variants, suggesting that these variables are intimately connected. Stopped-flow fluorescence spectroscopy shows that S16(meso) folds through an apparent two-state model, whereas S16(thermo) folds through a more complex mechanism with a marked curvature in the refolding limb indicating the presence of a folding intermediate. Time-resolved energy transfer between Trp and N-(4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene-3-yl)methyl iodoacetamide of proteins mutated at selected positions shows that the denatured state ensemble of S16(thermo) is more compact relative to S16(meso). Taken together, our results suggest the presence of residual structure in the denatured state ensemble of S16(thermo) that appears to account for the large difference in quantified DeltaC(p)(0) values and, in turn, parts of the observed extreme thermal stability of S16(thermo). These observations may be of general importance in the design of robust enzymes that are highly active over a wide temperature span.


    Organizational Affiliation

    Department of Chemistry, University of Umeå, SE-901 87 Umeå, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S16A112Aquifex aeolicusMutation(s): 0 
Gene Names: rpsP
Find proteins for O66523 (Aquifex aeolicus (strain VF5))
Explore O66523 
Go to UniProtKB:  O66523
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.241 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.5α = 90
b = 54.5β = 90
c = 74.9γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata scaling
XDSdata reduction
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2007-12-13 
  • Released Date: 2008-05-27 
  • Deposition Author(s): Pylypenko, O., Rak, A.

Revision History 

  • Version 1.0: 2008-05-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance