7L4K

Crystal structure of the DRM2-CCG DNA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 

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This is version 1.1 of the entry. See complete history


Literature

Substrate deformation regulates DRM2-mediated DNA methylation in plants.

Fang, J.Leichter, S.M.Jiang, J.Biswal, M.Lu, J.Zhang, Z.M.Ren, W.Zhai, J.Cui, Q.Zhong, X.Song, J.

(2021) Sci Adv 7

  • DOI: https://doi.org/10.1126/sciadv.abd9224
  • Primary Citation of Related Structures:  
    7L4C, 7L4F, 7L4H, 7L4K, 7L4M, 7L4N

  • PubMed Abstract: 

    DNA methylation is a major epigenetic mechanism critical for gene expression and genome stability. In plants, domains rearranged methyltransferase 2 (DRM2) preferentially mediates CHH (H = C, T, or A) methylation, a substrate specificity distinct from that of mammalian DNA methyltransferases. However, the underlying mechanism is unknown. Here, we report structure-function characterization of DRM2-mediated methylation. An arginine finger from the catalytic loop intercalates into the nontarget strand of DNA through the minor groove, inducing large DNA deformation that affects the substrate preference of DRM2. The target recognition domain stabilizes the enlarged major groove via shape complementarity rather than base-specific interactions, permitting substrate diversity. The engineered DRM2 C397R mutation introduces base-specific contacts with the +2-flanking guanine, thereby shifting the substrate specificity of DRM2 toward CHG DNA. Together, this study uncovers DNA deformation as a mechanism in regulating the specificity of DRM2 toward diverse CHH substrates and illustrates methylome complexity in plants.


  • Organizational Affiliation

    Department of Biochemistry, University of California, Riverside, Riverside, CA 92521, USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA (cytosine-5)-methyltransferase DRM2357Arabidopsis thalianaMutation(s): 0 
Gene Names: DRM2At5g14620/At5g14630T15N1.110/T15N1.120
EC: 2.1.1.37
UniProt
Find proteins for Q9M548 (Arabidopsis thaliana)
Explore Q9M548 
Go to UniProtKB:  Q9M548
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9M548
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*TP*AP*AP*AP*TP*TP*CP*GP*GP*AP*TP*TP*AP*GP*GP*AP*AP*T)-3')18Arabidopsis thaliana
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*TP*TP*CP*CP*TP*AP*AP*TP*(C49)P*CP*GP*AP*AP*TP*TP*TP*A)-3')18Arabidopsis thaliana
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.216 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 117.968α = 90
b = 231.582β = 90
c = 54.344γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
Cootmodel building
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R35GM119721

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description