6MIQ

Crystal structure of Taf14 YEATS domain in complex with histone H3K9bu

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

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Literature

Structural insights into the pi-pi-pi stacking mechanism and DNA-binding activity of the YEATS domain.

Klein, B.J., Vann, K.R., Andrews, F.H., Wang, W.W., Zhang, J., Zhang, Y., Beloglazkina, A.A., Mi, W., Li, Y., Li, H., Shi, X., Kutateladze, A.G., Strahl, B.D., Liu, W.R., Kutateladze, T.G.

(2018) Nat Commun 9: 4574-4574

  • DOI: 10.1038/s41467-018-07072-6
  • Primary Citation of Related Structures:  
    6MIL, 6MIM, 6MIN, 6MIO, 6MIP, 6MIQ

  • PubMed Abstract: 

    • The YEATS domain has been identified as a reader of histone acylation and more recently emerged as a promising anti-cancer therapeutic target. Here, we detail the structural mechanisms for π-π-π stacking involving the YEATS domains of yeast Taf14 and human AF9 and acylated histone H3 peptides and explore DNA-binding activities of these domains ...

    The YEATS domain has been identified as a reader of histone acylation and more recently emerged as a promising anti-cancer therapeutic target. Here, we detail the structural mechanisms for π-π-π stacking involving the YEATS domains of yeast Taf14 and human AF9 and acylated histone H3 peptides and explore DNA-binding activities of these domains. Taf14-YEATS selects for crotonyllysine, forming π stacking with both the crotonyl amide and the alkene moiety, whereas AF9-YEATS exhibits comparable affinities to saturated and unsaturated acyllysines, engaging them through π stacking with the acyl amide. Importantly, AF9-YEATS is capable of binding to DNA, whereas Taf14-YEATS is not. Using a structure-guided approach, we engineered a mutant of Taf14-YEATS that engages crotonyllysine through the aromatic-aliphatic-aromatic π stacking and shows high selectivity for the crotonyl H3K9 modification. Our findings shed light on the molecular principles underlying recognition of acyllysine marks and reveal a previously unidentified DNA-binding activity of AF9-YEATS.

    Organizational Affiliation: 

    Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA. tatiana.kutateladze@ucdenver.edu.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 14A142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TAF14, ANC1, CST10, SWP29, TAF30, TFG3, YPL129W
UniProt
Find proteins for P35189 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P35189 
Go to UniProtKB:  P35189
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35189
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3K9buB [auth C]8Homo sapiensMutation(s): 0 
Gene Names: 
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens)
Explore P68431 
Go to UniProtKB:  P68431
PHAROS:  P68431
GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775 
Entity Groups  
UniProt GroupP68431
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BTK
Query on BTK		B [auth C]L-PEPTIDE LINKINGC10 H20 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.149α = 90
b = 113.149β = 90
c = 26.17γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-14
    Type: Initial release