8V9U | pdb_00008v9u

Solution NMR structure of human DNMT1 N-terminal alpha-helical domain

• PDB DOI: https://doi.org/10.2210/pdb8V9U/pdb
• BMRB: 31134

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-12-09 Released: 2024-02-28 
• Deposition Author(s): Hu, Q., Botuyan, M.V., Mer, G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 30 
• Selection Criteria: structures with the lowest energy 

Literature

Identification of a conserved alpha-helical domain at the N terminus of human DNA methyltransferase 1.

Hu, Q., Botuyan, M.V., Mer, G.

(2024) J Biological Chem 300: 105775-105775

• PubMed: 38382673 
• DOI: https://doi.org/10.1016/j.jbc.2024.105775
• Primary Citation of Related Structures:  
  8V9U


• PubMed Abstract: 
  

  In vertebrates, DNA methyltransferase 1 (DNMT1) contributes to preserving DNA methylation patterns, ensuring the stability and heritability of epigenetic marks important for gene expression regulation and the maintenance of cellular identity. Previous structural studies have elucidated the catalytic mechanism of DNMT1 and its specific recognition of hemimethylated DNA. Here, using solution nuclear magnetic resonance spectroscopy and small-angle X-ray scattering, we demonstrate that the N-terminal region of human DNMT1, while flexible, encompasses a conserved globular domain with a novel α-helical bundle-like fold. This work expands our understanding of the structure and dynamics of DNMT1 and provides a structural framework for future functional studies in relation with this new domain.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, Minnesota, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: SAXS

Macromolecule Content

• Total Structure Weight: 9.49 kDa 
• Atom Count: 663 
• Modelled Residue Count: 81 
• Deposited Residue Count: 81 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA (cytosine-5)-methyltransferase 1	A	81	Homo sapiens	Mutation(s): 0  Gene Names: DNMT1, AIM, CXXC9, DNMT EC: 2.1.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for P26358 (Homo sapiens) Explore P26358  Go to UniProtKB:  P26358
PHAROS:  P26358 GTEx:  ENSG00000130816

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 30 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-28 
Deposition Author(s): Hu, Q., Botuyan, M.V., Mer, G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM136262
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	R01 CA132878

Revision History  

• Version 1.0: 2024-02-28
  Type: Initial release
  
• Version 1.1: 2024-05-15
  Changes: Database references
• Version 1.2: 2024-06-05
  Changes: Database references