1UCL

Mutants of RNase Sa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The contribution of polar group burial to protein stability is strongly context-dependent

Takano, K.Scholtz, J.M.Sacchettini, J.C.Pace, C.N.

(2003) J.Biol.Chem. 278: 31790-31795

  • DOI: 10.1074/jbc.M304177200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We previously suggested that proteins gain more stability from the burial and hydrogen bonding of polar groups than from the burial of nonpolar groups (Pace, C. N. (2001) Biochemistry 40, 310-313). To study this further, we prepared eight Thr-to-Val ...

    We previously suggested that proteins gain more stability from the burial and hydrogen bonding of polar groups than from the burial of nonpolar groups (Pace, C. N. (2001) Biochemistry 40, 310-313). To study this further, we prepared eight Thr-to-Val mutants of RNase Sa, four in which the Thr side chain is hydrogen-bonded and four in which it is not. We measured the stability of these mutants by analyzing their thermal denaturation curves. The four hydrogen-bonded Thr side chains contribute 1.3 +/- 0.9 kcal/mol to the stability; those that are not still contribute 0.4 +/- 0.9 kcal/mol to the stability. For 40 Thr-to-Val mutants of 11 proteins, the average decrease in stability is 1.0 +/- 1.0 kcal/mol when the Thr side chain is hydrogen-bonded and 0.0 +/- 0.5 kcal/mol when it is not. This is clear evidence that hydrogen bonds contribute favorably to protein stability. In addition, we prepared four Val-to-Thr mutants of RNase Sa, measured their stability, and determined their crystal structures. In all cases, the mutants are less stable than the wild-type protein, with the decreases in stability ranging from 0.5 to 4.4 kcal/mol. For 41 Val-to-Thr mutants of 11 proteins, the average decrease in stability is 1.8 +/- 1.3 kcal/mol and is unfavorable for 40 of 41 mutants. This shows that placing an [bond]OH group at a site designed for a [bond]CH3 group is very unfavorable. So, [bond]OH groups can contribute favorably to protein stability, even if they are not hydrogen-bonded, if the site was selected for an [bond]OH group, but they will make an unfavorable contribution to stability, even if they are hydrogen-bonded, when they are placed at a site selected for a [bond]CH3 group. The contribution that polar groups make to protein stability depends strongly on their environment.


    Organizational Affiliation

    Department of Material and Life Science, Osaka University, and Precursory Research for Embryonic Science and Technology, Japan Science and Technology Corporation, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Guanyl-specific ribonuclease Sa
A, B
96Kitasatospora aureofaciensMutation(s): 1 
Gene Names: rnaSA
EC: 3.1.27.3
Find proteins for P05798 (Kitasatospora aureofaciens)
Go to UniProtKB:  P05798
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.176 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 64.261α = 90.00
b = 77.658β = 90.00
c = 38.344γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-09-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance