5YY9 | pdb_00005yy9

Crystal structure of Tandem Tudor Domain of human UHRF1 in complex with LIG1-K126me3

• PDB DOI: https://doi.org/10.2210/pdb5YY9/pdb

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


• Deposited: 2017-12-08 Released: 2018-12-12 
• Deposition Author(s): Kori, S., Defossez, P.A., Arita, K.
• Funding Organization(s): JST

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free: 
  0.288 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.231 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

Structure of the UHRF1 Tandem Tudor Domain Bound to a Methylated Non-histone Protein, LIG1, Reveals Rules for Binding and Regulation.

Kori, S., Ferry, L., Matano, S., Jimenji, T., Kodera, N., Tsusaka, T., Matsumura, R., Oda, T., Sato, M., Dohmae, N., Ando, T., Shinkai, Y., Defossez, P.A., Arita, K.

(2019) Structure 27: 485

• PubMed: 30639225 
• DOI: https://doi.org/10.1016/j.str.2018.11.012
• Primary Citation Related Structures: 
  5YY9, 5YYA


• PubMed Abstract: 
  

  The protein UHRF1 is crucial for DNA methylation maintenance. The tandem Tudor domain (TTD) of UHRF1 binds histone H3K9me2/3 with micromolar affinity, as well as unmethylated linker regions within UHRF1 itself, causing auto-inhibition. Recently, we showed that a methylated histone-like region of DNA ligase 1 (LIG1K126me2/me3) binds the UHRF1 TTD with nanomolar affinity, permitting UHRF1 recruitment to chromatin. Here we report the crystal structure of the UHRF1 TTD bound to a LIG1K126me3 peptide. The data explain the basis for the high TTD-binding affinity of LIG1K126me3 and reveal that the interaction may be regulated by phosphorylation. Binding of LIG1K126me3 switches the overall structure of UHRF1 from a closed to a flexible conformation, suggesting that auto-inhibition is relieved. Our results provide structural insight into how UHRF1 performs its key function in epigenetic maintenance.

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Organizational Affiliation: 
• Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan.
University of Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 CNRS, 75013 Paris, France.
Bio-AFM Frontier Research Center, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan; WPI Nano Life Science Institute, Kakuma-machi, Kanazawa 920-1192, Japan; JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.
Cellular Memory Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan.
Biomolecular Characterization Unit, Technology Platform Division, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan.
Bio-AFM Frontier Research Center, Kanazawa University, Kakuma-machi, Kanazawa 920-1192, Japan; WPI Nano Life Science Institute, Kakuma-machi, Kanazawa 920-1192, Japan.
University of Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR 7216 CNRS, 75013 Paris, France. Electronic address: [e-mail].
Graduate School of Medical Life Science, Yokohama City University, Yokohama 230-0045, Japan; JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: isothermal titration calorimetry

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 39.6 kDa 
• Atom Count: 2,414 
• Modeled Residue Count: 297 
• Deposited Residue Count: 334 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase UHRF1	A, B	154	Homo sapiens	Mutation(s): 0  Gene Names: UHRF1, ICBP90, NP95, RNF106 EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q96T88 (Homo sapiens) Explore Q96T88  Go to UniProtKB:  Q96T88
PHAROS:  Q96T88 GTEx:  ENSG00000276043

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ligase 1	C, D	13	synthetic construct	Mutation(s): 0  EC: 6.5.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P18858 (Homo sapiens) Explore P18858  Go to UniProtKB:  P18858
PHAROS:  P18858 GTEx:  ENSG00000105486

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L	C, D	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.65 Å
• R-Value Free:  0.288 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.231 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 27.105	α = 90
b = 97.349	β = 90
c = 132.529	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-12-12 
Deposition Author(s): Kori, S., Defossez, P.A., Arita, K.

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Funding Organization	Location	Grant Number
JST	Japan	PRESTO 14530337

Revision History  

• Version 1.0: 2018-12-12
  Type: Initial release
  
• Version 1.1: 2019-01-23
  Changes: Data collection, Database references
• Version 1.2: 2019-03-20
  Changes: Data collection, Database references
• Version 1.3: 2023-11-22
  Changes: Data collection, Database references, Refinement description