6MR4

Crystal structure of the Sth1 bromodomain from S.cerevisiae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Substrate Affinity and Specificity of the ScSth1p Bromodomain Are Fine-Tuned for Versatile Histone Recognition.

Blus, B.J.Hashimoto, H.Seo, H.S.Krolak, A.Debler, E.W.

(2019) Structure 27: 1460-1468.e3

  • DOI: 10.1016/j.str.2019.06.009
  • Primary Citation of Related Structures:  
    6MR4

  • PubMed Abstract: 
  • Bromodomains recognize a wide range of acetylated lysines in histones and other nuclear proteins. Substrate specificity is critical for their biological function and arises from unique acetyl-lysine binding sites formed by variable loop regions. Here, we analyzed substrate affinity and specificity of the yeast ScSth1p bromodomain, an essential component of the "Remodels the Structure of Chromatin" complex, and found that the wild-type bromodomain preferentially recognizes H3K14ac and H4K20ac peptides ...

    Bromodomains recognize a wide range of acetylated lysines in histones and other nuclear proteins. Substrate specificity is critical for their biological function and arises from unique acetyl-lysine binding sites formed by variable loop regions. Here, we analyzed substrate affinity and specificity of the yeast ScSth1p bromodomain, an essential component of the "Remodels the Structure of Chromatin" complex, and found that the wild-type bromodomain preferentially recognizes H3K14ac and H4K20ac peptides. Mutagenesis studies-guided by our crystal structure determined at 2.7-Å resolution-revealed loop residues Ser1276 and Trp1338 as key determinants for such interactions. Strikingly, point mutations of each of these residues substantially increased peptide binding affinity and selectivity, respectively. Our data demonstrate that the ScSth1p bromodomain is not optimized for binding to an individual acetylation mark, but fine-tuned for interactions with several such modifications, consistent with the versatile and multivalent nature of histone recognition by reader modules such as bromodomains.


    Organizational Affiliation

    Department of Biochemistry & Molecular Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA. Electronic address: erik.debler@jefferson.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear protein STH1/NPS1A, B, C, D, E, F112Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: STH1NPS1YIL126W
EC: 3.6.4.12
UniProt
Find proteins for P32597 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32597 
Go to UniProtKB:  P32597
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.239 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.753α = 90
b = 74.619β = 92.88
c = 72.541γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
XDSdata scaling
XDSdata reduction
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.2: 2019-09-18
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-20
    Changes: Author supporting evidence