3PTA

Crystal structure of human DNMT1(646-1600) in complex with DNA

• PDB DOI: https://doi.org/10.2210/pdb3PTA/pdb
• NAKB: 3PTA

• Classification: Transferase/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-12-02 Released: 2010-12-29 
• Deposition Author(s): Song, J., Patel, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 0.291 
• R-Value Work: 0.257 
• R-Value Observed: 0.257 

Literature

Structure of DNMT1-DNA complex reveals a role for autoinhibition in maintenance DNA methylation.

Song, J., Rechkoblit, O., Bestor, T.H., Patel, D.J.

(2011) Science 331: 1036-1040

• PubMed: 21163962 
• DOI: https://doi.org/10.1126/science.1195380
• Primary Citation of Related Structures:  
  3PT6, 3PT9, 3PTA


• PubMed Abstract: 
  

  Maintenance of genomic methylation patterns is mediated primarily by DNA methyltransferase-1 (DNMT1). We have solved structures of mouse and human DNMT1 composed of CXXC, tandem bromo-adjacent homology (BAH1/2), and methyltransferase domains bound to DNA-containing unmethylated CpG sites. The CXXC specifically binds to unmethylated CpG dinucleotide and positions the CXXC-BAH1 linker between the DNA and the active site of DNMT1, preventing de novo methylation. In addition, a loop projecting from BAH2 interacts with the target recognition domain (TRD) of the methyltransferase, stabilizing the TRD in a retracted position and preventing it from inserting into the DNA major groove. Our studies identify an autoinhibitory mechanism, in which unmethylated CpG dinucleotides are occluded from the active site to ensure that only hemimethylated CpG dinucleotides undergo methylation.

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Organizational Affiliation: 

Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 120.36 kDa 
• Atom Count: 7,989 
• Modelled Residue Count: 942 
• Deposited Residue Count: 994 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA (cytosine-5)-methyltransferase 1	A	956	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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*CP*CP*GP*TP*GP*AP*GP*CP*CP*TP*CP*CP*GP*CP*AP*GP*G)-3')	B	19	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*TP*GP*CP*GP*GP*AP*GP*GP*CP*TP*CP*AP*CP*GP*GP*GP*A)-3')	C	19	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	D [auth A]	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N
ZN	E [auth A], F [auth A], G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SAH	BindingDB:  3PTA	IC50: min: 71, max: 4000 (nM) from 8 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.60 Å
• R-Value Free: 0.291 
• R-Value Work: 0.257 
• R-Value Observed: 0.257 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.8	α = 90
b = 87.9	β = 97.2
c = 113.9	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-12-29 
Deposition Author(s): Song, J., Patel, D.J.

Revision History  

• Version 1.0: 2010-12-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations