7W5P

Crystal Structure of the dioxygenase CcTet from Coprinopsis cinereain bound to 12bp N6-methyldeoxyadenine (6mA) containing duplex DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

A fungal dioxygenase CcTet serves as a eukaryotic 6mA demethylase on duplex DNA.

Mu, Y.Zhang, L.Hu, J.Zhou, J.Lin, H.W.He, C.Chen, H.Z.Zhang, L.

(2022) Nat Chem Biol 18: 733-741

  • DOI: https://doi.org/10.1038/s41589-022-01041-3
  • Primary Citation of Related Structures:  
    7VPN, 7W5P

  • PubMed Abstract: 

    N 6 -methyladenosine (6mA) is a DNA modification that has recently been found to play regulatory roles during mammalian early embryo development and mitochondrial transcription. We found that a dioxygenase CcTet from the fungus Coprinopsis cinerea is also a dsDNA 6mA demethylase. It oxidizes 6mA to the intermediate N 6 -hydroxymethyladenosine (6hmA) with robust activity of 6mA-containing duplex DNA (dsDNA) as well as isolated genomics DNA. Structural characterization revealed that CcTet utilizes three flexible loop regions and two key residues-D337 and G331-in the active pocket to preferentially recognize substrates on dsDNA. A CcTet D337F mutant protein retained the catalytic activity on 6mA but lost activity on 5-methylcytosine. Our findings uncovered a 6mA demethylase that works on dsDNA, suggesting potential 6mA demethylation in fungi and elucidating 6mA recognition and the catalytic mechanism of CcTet. The CcTet D337F mutant protein also provides a chemical biology tool for future functional manipulation of DNA 6mA in vivo.


  • Organizational Affiliation

    Department of Pharmacology and Chemical Biology, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, Shanghai, China.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CcTet
A, D, G, H
430Coprinopsis cinereaMutation(s): 0 
Gene Names: CC1G_05589
UniProt
Find proteins for A8P1J0 (Coprinopsis cinerea (strain Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003))
Explore A8P1J0 
Go to UniProtKB:  A8P1J0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8P1J0
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (12-MER)
B, E
12synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA
C, F
12synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.788α = 90
b = 105.198β = 90
c = 196.717γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China91853118
National Natural Science Foundation of China (NSFC)China22107067
National Natural Science Foundation of China (NSFC)China22077081
National Natural Science Foundation of China (NSFC)China21722802

Revision History  (Full details and data files)

  • Version 1.0: 2022-03-30
    Type: Initial release
  • Version 1.1: 2022-06-15
    Changes: Database references
  • Version 1.2: 2022-07-06
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description