Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B 

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

Macromolecule Content

• Total Structure Weight: 49116.05 
• Atom Count: 3165 
• Residue Count: 439 
• Unique protein chains: 3

5WVO

Crystal structure of DNMT1 RFTS domain in complex with K18/K23 mono-ubiquitylated histone H3

• DOI: 10.2210/pdb5WVO/pdb

• Classification: SIGNALING PROTEIN/TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpT4
• Mutation(s): 3 


• Deposited: 2016-12-28 Released: 2017-11-15 
• Deposition Author(s): Ishiyama, S., Nishiyama, A., Nakanishi, M., Arita, K.
• Funding Organization(s): JST PRESTO 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.997 Å
• R-Value Free: 0.239 
• R-Value Work: 0.196 

Literature

Structure of the Dnmt1 Reader Module Complexed with a Unique Two-Mono-Ubiquitin Mark on Histone H3 Reveals the Basis for DNA Methylation Maintenance

Ishiyama, S., Nishiyama, A., Saeki, Y., Moritsugu, K., Morimoto, D., Yamaguchi, L., Arai, N., Matsumura, R., Kawakami, T., Mishima, Y., Hojo, H., Shimamura, S., Ishikawa, F., Tajima, S., Tanaka, K., Ariyoshi, M., Shirakawa, M., Ikeguchi, M., Kidera, A., Suetake, I., Arita, K., Nakanishi, M.

(2017) Mol. Cell 68: 350-360.e7

• PubMed: 29053958 
• DOI: 10.1016/j.molcel.2017.09.037


• PubMed Abstract: 
  

The proper location and timing of Dnmt1 activation are essential for DNA methylation maintenance. We demonstrate here that Dnmt1 utilizes two-mono-ubiquitylated histone H3 as a unique ubiquitin mark for its recruitment to and activation at DNA methylation sites. The crystal structure of the replication foci targeting sequence (RFTS) of Dnmt1 in complex with H3-K18Ub/23Ub reveals striking differences to the known ubiquitin-recognition structures. The two ubiquitins are simultaneously bound to the RFTS with a combination of canonical hydrophobic and atypical hydrophilic interactions. The C-lobe of RFTS, together with the K23Ub surface, also recognizes the N-terminal tail of H3. The binding of H3-K18Ub/23Ub results in spatial rearrangement of two lobes in the RFTS, suggesting the opening of its active site. Actually, incubation of Dnmt1 with H3-K18Ub/23Ub increases its catalytic activity in vitro. Our results therefore shed light on the essential role of a unique ubiquitin-binding module in DNA methylation maintenance.

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Organizational Affiliation: 

Structure Biology Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Ubiquitin	A, B	76	Homo sapiens	Mutation(s): 1  Gene Names: RPS27A (UBA80, UBCEP1)
Find proteins for P62979 (Homo sapiens) Go to Gene View: RPS27A Go to UniProtKB:  P62979

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
DNA (cytosine-5)-methyltransferase 1	C	250	Homo sapiens	Mutation(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: 3
Molecule	Chains	Sequence Length	Organism	Details
Histone H3.1	D	37	Homo sapiens	Mutation(s): 2  Gene Names: HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J (H3FA, H3FL, H3FC, H3FB, H3FD, H3FI, H3FH, H3FK, H3FF, H3FJ)
Find proteins for P68431 (Homo sapiens) Go to Gene View: HIST1H3A HIST1H3B HIST1H3C HIST1H3D HIST1H3E HIST1H3F HIST1H3G HIST1H3H HIST1H3I HIST1H3J Go to UniProtKB:  P68431

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	C	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.997 Å
• R-Value Free: 0.239 
• R-Value Work: 0.196 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 68.362	α = 90.00
b = 198.779	β = 90.00
c = 76.904	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
HKL-2000	data reduction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-12-28 
• Released Date: 2017-11-15 
• Deposition Author(s): Ishiyama, S., Nishiyama, A., Nakanishi, M., Arita, K.

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Funding Organization	Location	Grant Number
JST PRESTO	Japan	--

Revision History 

• Version 1.0: 2017-11-15
  Type: Initial release