4YGI

Crystal Structure of SUVH5 SRA bound to fully hydroxymethylated CG DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.237 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Mechanistic insights into the recognition of 5-methylcytosine oxidation derivatives by the SUVH5 SRA domain

Rajakumara, E.Nakarakanti, N.K.Nivya, M.A.Satish, M.

(2016) Sci Rep 6: 20161-20161

  • DOI: 10.1038/srep20161
  • Primary Citation of Related Structures:  
    4YGI

  • PubMed Abstract: 
  • 5-Methylcytosine (5 mC) is associated with epigenetic gene silencing in mammals and plants. 5 mC is consecutively oxidized to 5-hydroxymethylcytosine (5 hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) by ten-eleven translocation enzymes. We performed binding and structural studies to investigate the molecular basis of the recognition of the 5 mC oxidation derivatives in the context of a CG sequence by the SET- and RING-associated domain (SRA) of the SUVH5 protein (SUVH5 SRA) ...

    5-Methylcytosine (5 mC) is associated with epigenetic gene silencing in mammals and plants. 5 mC is consecutively oxidized to 5-hydroxymethylcytosine (5 hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) by ten-eleven translocation enzymes. We performed binding and structural studies to investigate the molecular basis of the recognition of the 5 mC oxidation derivatives in the context of a CG sequence by the SET- and RING-associated domain (SRA) of the SUVH5 protein (SUVH5 SRA). Using calorimetric measurements, we demonstrate that the SRA domain binds to the hydroxymethylated CG (5hmCG) DNA duplex in a similar manner to methylated CG (5mCG). Interestingly, the SUVH5 SRA domain exhibits weaker affinity towards carboxylated CG (5caCG) and formylated CG (5fCG). We report the 2.6 Å resolution crystal structure of the SUVH5 SRA domain in a complex with fully hydroxymethyl-CG and demonstrate a dual flip-out mechanism, whereby the symmetrical 5hmCs are simultaneously extruded from the partner strands of the DNA duplex and are positioned within the binding pockets of individual SRA domains. The hydroxyl group of 5hmC establishes both intra- and intermolecular interactions in the binding pocket. Collectively, we show that SUVH5 SRA recognizes 5hmC in a similar manner to 5 mC, but exhibits weaker affinity towards 5 hmC oxidation derivatives.


    Organizational Affiliation

    Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502285, Telangana, India.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-9 specific SUVH5A167Arabidopsis thalianaMutation(s): 0 
Gene Names: SUVH5SDG9SET9At2g35160T4C15.17
EC: 2.1.1.43 (PDB Primary Data), 2.1.1 (UniProt)
UniProt
Find proteins for O82175 (Arabidopsis thaliana)
Explore O82175 
Go to UniProtKB:  O82175
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    PolydeoxyribonucleotideB11synthetic construct
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    C [auth A], D [auth B], E [auth B]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.60 Å
    • R-Value Free: 0.283 
    • R-Value Work: 0.234 
    • R-Value Observed: 0.237 
    • Space Group: P 42 21 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 76.98α = 90
    b = 76.98β = 90
    c = 72.111γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-2000data scaling
    MOLREPphasing
    PDB_EXTRACTdata extraction
    HKL-2000data reduction

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    • Deposited Date: 2015-02-26 
    • Released Date: 2016-02-17 
    • Deposition Author(s): Rajakumara, E.

    Revision History  (Full details and data files)

    • Version 1.0: 2016-02-17
      Type: Initial release
    • Version 1.1: 2016-03-02
      Changes: Database references