6AT0

Chromodomain HP1 with a p-nitro-L-phenylalanine mutation at position 24 bound to histone H3 peptide containing trimethyl lysine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.285 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.241 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Investigation of Trimethyllysine Binding by the HP1 Chromodomain via Unnatural Amino Acid Mutagenesis.

Baril, S.A., Koenig, A.L., Krone, M.W., Albanese, K.I., He, C.Q., Lee, G.Y., Houk, K.N., Waters, M.L., Brustad, E.M.

(2017) J. Am. Chem. Soc. 139: 17253-17256

  • DOI: 10.1021/jacs.7b09223
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Trimethyllysine (Kme3) reader proteins are targets for inhibition due to their role in mediating gene expression. Although all such reader proteins bind Kme3 in an aromatic cage, the driving force for binding may differ; some readers exhibit evidence ...

    Trimethyllysine (Kme3) reader proteins are targets for inhibition due to their role in mediating gene expression. Although all such reader proteins bind Kme3 in an aromatic cage, the driving force for binding may differ; some readers exhibit evidence for cation-π interactions whereas others do not. We report a general unnatural amino acid mutagenesis approach to quantify the contribution of individual tyrosines to cation binding using the HP1 chromodomain as a model system. We demonstrate that two tyrosines (Y24 and Y48) bind to a Kme3-histone tail peptide via cation-π interactions, but linear free energy trends suggest they do not contribute equally to binding. X-ray structures and computational analysis suggest that the distance and degree of contact between Tyr residues and Kme3 plays an important role in tuning cation-π-mediated Kme3 recognition. Although cation-π interactions have been studied in a number of proteins, this work is the first to utilize direct binding assays, X-ray crystallography, and modeling, to pinpoint factors that influence the magnitude of the individual cation-π interactions.

    Organizational Affiliation: 

    Department of Chemistry, CB 3290, University of North Carolina at Chapel Hill , Chapel Hill, North Carolina 27599, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Heterochromatin protein 1
A
69Drosophila melanogasterMutation(s): 2 
Gene Names: Su(var)205 (HP1)
Find proteins for P05205 (Drosophila melanogaster)
Go to UniProtKB:  P05205
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
trimethyl lysine histone H3 tail peptide
P
6Drosophila melanogasterMutation(s): 0 
Gene Names: His3, His3:CG31613, His3:CG33803, His3:CG33806, His3:CG33809, His3:CG33812, His3:CG33815, His3:CG33818, His3:CG33821, His3:CG33824, His3:CG33827, His3:CG33830, His3:CG33833, His3:CG33836, His3:CG33839, His3:CG33842, His3:CG33845, His3:CG33848, His3:CG33851, His3:CG33854, His3:CG33857, His3:CG33860, His3:CG33863, His3:CG33866
Find proteins for P02299 (Drosophila melanogaster)
Go to UniProtKB:  P02299
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
P
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
PPN
Query on PPN
A
L-PEPTIDE LINKINGC9 H10 N2 O4PHE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.285 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.241 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 34.417α = 90.00
b = 76.857β = 90.00
c = 76.479γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-06
    Type: Initial release
  • Version 1.1: 2017-12-13
    Type: Database references