5IAY | pdb_00005iay

NMR structure of UHRF1 Tandem Tudor Domains in a complex with Spacer peptide

• PDB DOI: https://doi.org/10.2210/pdb5IAY/pdb
• BMRB: 30019

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


• Deposited: 2016-02-22 Released: 2016-04-20 
• Deposition Author(s): Fang, J., Cheng, J., Wang, J., Zhang, Q., Liu, M., Gong, R., Wang, P., Zhang, X., Feng, Y., Lan, W., Gong, Z., Tang, C., Wong, J., Yang, H., Cao, C., Xu, Y.
• Funding Organization(s): National Basic Research Program of China

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

Hemi-methylated DNA opens a closed conformation of UHRF1 to facilitate its histone recognition

Fang, J., Cheng, J., Wang, J., Zhang, Q., Liu, M., Gong, R., Wang, P., Zhang, X., Feng, Y., Lan, W., Gong, Z., Tang, C., Wong, J., Yang, H., Cao, C., Xu, Y.

(2016) Nat Commun 7: 11197-11197

• PubMed: 27045799 
• DOI: https://doi.org/10.1038/ncomms11197
• Primary Citation Related Structures: 
  5IAY


• PubMed Abstract: 
  

  UHRF1 is an important epigenetic regulator for maintenance DNA methylation. UHRF1 recognizes hemi-methylated DNA (hm-DNA) and trimethylation of histone H3K9 (H3K9me3), but the regulatory mechanism remains unknown. Here we show that UHRF1 adopts a closed conformation, in which a C-terminal region (Spacer) binds to the tandem Tudor domain (TTD) and inhibits H3K9me3 recognition, whereas the SET-and-RING-associated (SRA) domain binds to the plant homeodomain (PHD) and inhibits H3R2 recognition. Hm-DNA impairs the intramolecular interactions and promotes H3K9me3 recognition by TTD-PHD. The Spacer also facilitates UHRF1-DNMT1 interaction and enhances hm-DNA-binding affinity of the SRA. When TTD-PHD binds to H3K9me3, SRA-Spacer may exist in a dynamic equilibrium: either recognizes hm-DNA or recruits DNMT1 to chromatin. Our study reveals the mechanism for regulation of H3K9me3 and hm-DNA recognition by URHF1.

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Organizational Affiliation: 
• 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.
State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China.
Fudan University Shanghai Cancer Center, Institute of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China.
State Key Laboratory of Bio-organic and Natural Product Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 LingLing Road, Shanghai 200032, China.
Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.
State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 19.41 kDa 
• Atom Count: 1,365 
• Modeled Residue Count: 168 
• Deposited Residue Count: 168 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase UHRF1	A	152	Homo sapiens	Mutation(s): 0  Gene Names: UHRF1, ICBP90, NP95, RNF106 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
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
Spacer	B	16	Homo sapiens	Mutation(s): 0  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

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-04-20 
Deposition Author(s): Fang, J., Cheng, J., Wang, J., Zhang, Q., Liu, M., Gong, R., Wang, P., Zhang, X., Feng, Y., Lan, W., Gong, Z., Tang, C., Wong, J., Yang, H., Cao, C., Xu, Y.

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Funding Organization	Location	Grant Number
National Basic Research Program of China	China	2011CB965300
National Basic Research Program of China	China	2011CB966300

Revision History  

• Version 1.0: 2016-04-20
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references, Structure summary