5WLF

Crystal structure of the apo PPS PHD finger

  • Classification: HYDROLASE
  • Organism(s): Drosophila melanogaster
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2017-07-26 Released: 2017-10-04 
  • Deposition Author(s): Klein, B.J., Kutateladze, T.G.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.138 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A Unique pH-Dependent Recognition of Methylated Histone H3K4 by PPS and DIDO.

Tencer, A.H.Gatchalian, J.Klein, B.J.Khan, A.Zhang, Y.Strahl, B.D.van Wely, K.H.M.Kutateladze, T.G.

(2017) Structure 25: 1530-1539.e3

  • DOI: https://doi.org/10.1016/j.str.2017.08.009
  • Primary Citation of Related Structures:  
    5WLE, 5WLF

  • PubMed Abstract: 

    The protein partner of Sans-fille (PPS) and its human homolog DIDO mediate diverse chromatin activities, including the regulation of stemness genes in embryonic stem cells and splicing in Drosophila. Here, we show that the PHD fingers of PPS and DIDO recognize the histone mark H3K4me3 in a pH-dependent manner: the binding is enhanced at high pH values but is decreased at low pH. Structural analysis reveals that the pH dependency is due to the presence of a histidine residue in the K4me3-binding aromatic cage of PPS. The pH-dependent mechanism is conserved in DIDO but is lost in yeast Bye1. Acidification of cells leads to the accelerated efflux of endogenous DIDO, indicating the pH-dependent sensing of H3K4me3 in vivo. This novel mode for the recognition of H3K4me3 establishes the PHD fingers of PPS and DIDO as unique epigenetic readers and high pH sensors and suggests a role for the histidine switch during mitosis.


  • Organizational Affiliation

    Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein partner of snf, isoform A62Drosophila melanogasterMutation(s): 0 
Gene Names: ppsCG6525Dmel_CG6525
EC: 3.6
UniProt
Find proteins for Q9VG78 (Drosophila melanogaster)
Explore Q9VG78 
Go to UniProtKB:  Q9VG78
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9VG78
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.160 
  • R-Value Work: 0.136 
  • R-Value Observed: 0.138 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 23.02α = 90
b = 41.06β = 98.43
c = 26.41γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
d*TREKdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM106416
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM101664
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM100907
National Institutes of Health/National Institute on Alcohol Abuse and Alcoholism (NIH/NIAAA)United StatesT32AA007464

Revision History  (Full details and data files)

  • Version 1.0: 2017-10-04
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Author supporting evidence, Database references
  • Version 1.2: 2019-12-11
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description