1XX8

NMR Structure of the W24A Mutant of the Hyperthermophile Sac7d Protein


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 11 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Role of a surface tryptophan in defining the structure, stability, and DNA binding of the hyperthermophile protein sac7d

Bedell, J.L.Edmondson, S.P.Shriver, J.W.

(2005) Biochemistry 44: 915-925

  • DOI: 10.1021/bi047823b
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Sac7d is a small, chromatin protein from Sulfolobus acidocaldarius which induces a sharp kink in DNA with intercalation of valine and methionine side chains. The crystal structure of the protein-DNA complex indicates that a surface tryptophan (W24) p ...

    Sac7d is a small, chromatin protein from Sulfolobus acidocaldarius which induces a sharp kink in DNA with intercalation of valine and methionine side chains. The crystal structure of the protein-DNA complex indicates that a surface tryptophan (W24) plays a key role in DNA binding by hydrogen bonding to the DNA at the kink site. We show here that substitution of the solvent-exposed tryptophan with alanine (W24A) led to a significant loss in not only DNA binding affinity but also protein stability. The W24A substitution proved to be one of the most destabilizing surface substitutions in Sac7d. A global linkage analysis of the pH and salt dependence of stability indicated that the protein stability surface (DeltaG vs temperature, pH, and salt concentration) was lowered overall by 2 kcal/mol (from 0 to 100 degrees C, pH 0 to 7, and 0 to 0.3 M KCl). The lower free energy of unfolding could not be attributed to significant structural perturbations of surface electrostatic interactions. Residual dipolar coupling of partially aligned protein and the NMR solution structure of W24A confirmed that the surface substitution resulted in no significant change in structure. Stabilization of this hyperthermophile protein and its DNA complex by a surface cluster of hydrophobic residues involving W24 and the two intercalating side chains is discussed.


    Organizational Affiliation

    Laboratory for Structural Biology, Department of Chemistry, Graduate Program in Biotechnology and Bioengineering, University of Alabama, Huntsville, Alabama 35899, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sac7d
A
66Sulfolobus acidocaldariusMutation(s): 1 
Gene Names: sac7d
Find proteins for P13123 (Sulfolobus acidocaldarius (strain ATCC 33909 / DSM 639 / JCM 8929 / NBRC 15157 / NCIMB 11770))
Go to UniProtKB:  P13123
Protein Feature View
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 11 
  • Selection Criteria: structures with the least restraint violations 
  • OLDERADO: 1XX8 Olderado

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-08
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance