3ASK

Structure of UHRF1 in complex with histone tail

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.904 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Recognition of modification status on a histone H3 tail by linked histone reader modules of the epigenetic regulator UHRF1

Arita, K., Isogai, S., Oda, T., Unoki, M., Sugita, K., Sekiyama, N., Kuwata, K., Hamamoto, R., Tochio, H., Sato, M., Ariyoshi, M., Shirakawa, M.

(2012) Proc.Natl.Acad.Sci.USA 109: 12950-12955

  • DOI: 10.1073/pnas.1203701109
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Multiple covalent modifications on a histone tail are often recognized by linked histone reader modules. UHRF1 [ubiquitin-like, containing plant homeodomain (PHD) and really interesting new gene (RING) finger domains 1], an essential factor for maint ...

    Multiple covalent modifications on a histone tail are often recognized by linked histone reader modules. UHRF1 [ubiquitin-like, containing plant homeodomain (PHD) and really interesting new gene (RING) finger domains 1], an essential factor for maintenance of DNA methylation, contains linked two-histone reader modules, a tandem Tudor domain and a PHD finger, tethered by a 17-aa linker, and has been implicated to link histone modifications and DNA methylation. Here, we present the crystal structure of the linked histone reader modules of UHRF1 in complex with the amino-terminal tail of histone H3. Our structural and biochemical data provide the basis for combinatorial readout of unmodified Arg-2 (H3-R2) and methylated Lys-9 (H3-K9) by the tandem tudor domain and the PHD finger. The structure reveals that the intermodule linker plays an essential role in the formation of a histone H3-binding hole between the reader modules by making extended contacts with the tandem tudor domain. The histone H3 tail fits into the hole by adopting a compact fold harboring a central helix, which allows both of the reader modules to simultaneously recognize the modification states at H3-R2 and H3-K9. Our data also suggest that phosphorylation of a linker residue can modulate the relative position of the reader modules, thereby altering the histone H3-binding mode. This finding implies that the linker region plays a role as a functional switch of UHRF1 involved in multiple regulatory pathways such as maintenance of DNA methylation and transcriptional repression.

    Organizational Affiliation: 

    Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase UHRF1
A, B, C, D
226Homo sapiensMutation(s): 0 
Gene Names: UHRF1 (ICBP90, NP95, RNF106)
EC: 2.3.2.27
Find proteins for Q96T88 (Homo sapiens)
Go to Gene View: UHRF1
Go to UniProtKB:  Q96T88
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3.3
P, Q, R
13Homo sapiensMutation(s): 0 
Gene Names: H3F3A, H3F3B (H3.3A, H3F3, H3.3B)
Find proteins for P84243 (Homo sapiens)
Go to Gene View: H3F3A H3F3B
Go to UniProtKB:  P84243
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
P, Q, R
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.904 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.243 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 145.178α = 90.00
b = 145.178β = 90.00
c = 125.413γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
ADSCdata collection
PHASERphasing
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-01-25
    Type: Initial release
  • Version 1.1: 2012-08-15
    Type: Database references
  • Version 1.2: 2013-06-05
    Type: Database references