4YOC

Crystal Structure of human DNMT1 and USP7/HAUSP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.916 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Molecular mechanism for USP7-mediated DNMT1 stabilization by acetylation.

Cheng, J.Yang, H.Fang, J.Ma, L.Gong, R.Wang, P.Li, Z.Xu, Y.

(2015) Nat Commun 6: 7023-7023

  • DOI: 10.1038/ncomms8023

  • PubMed Abstract: 
  • DNMT1 is an important epigenetic regulator that plays a key role in the maintenance of DNA methylation. Here we determined the crystal structure of DNMT1 in complex with USP7 at 2.9 Å resolution. The interaction between the two proteins is primarily ...

    DNMT1 is an important epigenetic regulator that plays a key role in the maintenance of DNA methylation. Here we determined the crystal structure of DNMT1 in complex with USP7 at 2.9 Å resolution. The interaction between the two proteins is primarily mediated by an acidic pocket in USP7 and Lysine residues within DNMT1's KG linker. This intermolecular interaction is required for USP7-mediated stabilization of DNMT1. Acetylation of the KG linker Lysine residues impair DNMT1-USP7 interaction and promote the degradation of DNMT1. Treatment with HDAC inhibitors results in an increase in acetylated DNMT1 and decreased total DNMT1 protein. This negative correlation is observed in differentiated neuronal cells and pancreatic cancer cells. Our studies reveal that USP7-mediated stabilization of DNMT1 is regulated by acetylation and provide a structural basis for the design of inhibitors, targeting the DNMT1-USP7 interaction surface for therapeutic applications.


    Organizational Affiliation

    1] Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, 131 Dong An Road, Mingdao Building, Room 715, Shanghai 200032, China [2] Key Laboratory of Molecular Medicine, Ministry of Education, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China [3] State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA (cytosine-5)-methyltransferase 1
A
1004Homo sapiensMutation(s): 0 
Gene Names: DNMT1 (AIM, CXXC9, DNMT)
EC: 2.1.1.37
Find proteins for P26358 (Homo sapiens)
Go to Gene View: DNMT1
Go to UniProtKB:  P26358
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin carboxyl-terminal hydrolase 7
C
548Homo sapiensMutation(s): 0 
Gene Names: USP7 (HAUSP)
EC: 3.4.19.12
Find proteins for Q93009 (Homo sapiens)
Go to Gene View: USP7
Go to UniProtKB:  Q93009
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.916 Å
  • R-Value Free: 0.258 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 110.231α = 90.00
b = 111.619β = 90.00
c = 163.868γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-27
    Type: Initial release