6JV3

Crystal structure of 5-hydoxylmethylcytosine containing decamer dsDNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.231 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Thymine DNA glycosylase recognizes the geometry alteration of minor grooves induced by 5-formylcytosine and 5-carboxylcytosine.

Fu, T.Liu, L.Yang, Q.L.Wang, Y.Xu, P.Zhang, L.Liu, S.Dai, Q.Ji, Q.Xu, G.L.He, C.Luo, C.Zhang, L.

(2019) Chem Sci 10: 7407-7417

  • DOI: 10.1039/c9sc02807b
  • Primary Citation of Related Structures:  
    6JV3, 6JV5, 5ZAT, 5ZAS

  • PubMed Abstract: 
  • The dynamic DNA methylation-demethylation process plays critical roles in gene expression control and cell development. The oxidation derivatives of 5-methylcytosine (5mC) generated by Tet dioxygenases in the demethylation pathway, namely 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), could impact biological functions by altering DNA properties or recognition by potential reader proteins ...

    The dynamic DNA methylation-demethylation process plays critical roles in gene expression control and cell development. The oxidation derivatives of 5-methylcytosine (5mC) generated by Tet dioxygenases in the demethylation pathway, namely 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), could impact biological functions by altering DNA properties or recognition by potential reader proteins. Hence, in addition to the fifth base 5mC, 5hmC, 5fC, and 5caC have been considered as the sixth, seventh, and eighth bases of the genome. How these modifications would alter DNA and be specifically recognized remain unclear, however. Here we report that formyl- and carboxyl-modifications on cytosine induce the geometry alteration of the DNA minor groove by solving two high-resolution structures of a dsDNA decamer containing fully symmetric 5fC and 5caC. The alterations are recognized distinctively by thymine DNA glycosylase TDG via its finger residue R275, followed by subsequent preferential base excision and DNA repair. These observations suggest a mechanism by which reader proteins distinguish highly similar cytosine modifications for potential differential demethylation in order to achieve downstream biological functions.


    Organizational Affiliation

    Shanghai Universities Collaborative Innovation Center for Translational Medicine , Shanghai , P. R. China.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*CP*AP*GP*(5HC)P*GP*CP*TP*GP*G)-3')A, B, C, D10Homo sapiens
    Protein Feature View
    Expand
    • Reference Sequence
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.85 Å
    • R-Value Free: 0.282 
    • R-Value Work: 0.228 
    • R-Value Observed: 0.231 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 63.907α = 90
    b = 23.818β = 111.12
    c = 85.556γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-3000data reduction
    HKL-3000data scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report




    Entry History & Funding Information

    Deposition Data

    • Deposited Date: 2019-04-15 
    • Released Date: 2019-07-31 
    • Deposition Author(s): Zhang, L., Wang, Y.X.

    Funding OrganizationLocationGrant Number
    National Natural Science Foundation of ChinaChina21572133
    National Natural Science Foundation of ChinaChina21722802

    Revision History  (Full details and data files)

    • Version 1.0: 2019-07-31
      Type: Initial release
    • Version 1.1: 2019-09-25
      Changes: Data collection, Database references