5ZAS

Crystal structure of 5-formylcytosine containing decamer dsDNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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-hydroxyme ...

    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

    Department of Chemistry , Department of Biochemistry and Molecular Biology , Institute for Biophysical Dynamics , The University of Chicago , Chicago , Illinois , USA.,University of Chinese Academy of Sciences , Beijing 100049 , China.,Department of Pharmacology and Chemical Biology , Shanghai Jiao Tong University School of Medicine , Shanghai , P. R. China . Email: liangzhang2014@sjtu.edu.cn ; Email: cluo@simm.ac.cn.,School of Physical Science and Technology , ShanghaiTech University , Shanghai , China.,Shanghai Universities Collaborative Innovation Center for Translational Medicine , Shanghai , P. R. China.,CAS Key Laboratory of Receptor Research , State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , Shanghai , China.,State Key Laboratory of Molecular Biology , Chinese Academy of Sciences Center for Excellence in Molecular Cell Science , Shanghai Institute of Biochemistry and Cell Biology , Chinese Academy of Sciences , University of Chinese Academy of Sciences , Shanghai , China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*CP*AP*GP*(5FC)P*GP*CP*TP*GP*G)-3')A,B10Homo sapiens
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BCT
Query on BCT

Download SDF File 
Download CCD File 
A
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5FC
Query on 5FC
A, B
DNA LINKINGC10 H14 N3 O8 PDC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.147 
  • Space Group: P 61
Unit Cell:
Length (Å)Angle (°)
a = 54.548α = 90.00
b = 54.548β = 90.00
c = 45.819γ = 120.00
Software Package:
Software NamePurpose
PHENIXphasing
PHENIXrefinement
HKL-3000data scaling
HKL-3000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-02-08 
  • Released Date: 2019-02-13 
  • Deposition Author(s): Fu, T.R., Zhang, L.

Revision History 

  • Version 1.0: 2019-02-13
    Type: Initial release
  • Version 1.1: 2019-08-28
    Type: Data collection, Database references
  • Version 1.2: 2019-09-18
    Type: Data collection, Database references