4O6F

Structural Basis of Estrogen Receptor Alpha Methylation Mediated by Histone Methyltransferase SmyD2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.822 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Insights into Estrogen Receptor alpha Methylation by Histone Methyltransferase SMYD2, a Cellular Event Implicated in Estrogen Signaling Regulation.

Jiang, Y.Trescott, L.Holcomb, J.Zhang, X.Brunzelle, J.Sirinupong, N.Shi, X.Yang, Z.

(2014) J.Mol.Biol. 426: 3413-3425

  • DOI: 10.1016/j.jmb.2014.02.019

  • PubMed Abstract: 
  • Estrogen receptor (ER) signaling plays a pivotal role in many developmental processes and has been implicated in numerous diseases including cancers. We recently showed that direct ERα methylation by the multi-specificity histone lysine methyltransfe ...

    Estrogen receptor (ER) signaling plays a pivotal role in many developmental processes and has been implicated in numerous diseases including cancers. We recently showed that direct ERα methylation by the multi-specificity histone lysine methyltransferase SMYD2 regulates estrogen signaling through repressing ERα-dependent transactivation. However, the mechanism controlling the specificity of the SMYD2-ERα interaction and the structural basis of SMYD2 substrate binding diversity are unknown. Here we present the crystal structure of SMYD2 in complex with a target lysine (Lys266)-containing ERα peptide. The structure reveals that ERα binds SMYD2 in a U-shaped conformation with the binding specificity determined mainly by residues C-terminal to the target lysine. The structure also reveals numerous intrapeptide contacts that ensure shape complementarity between the substrate and the active site of the enzyme, thereby likely serving as an additional structural determinant of substrate specificity. In addition, comparison of the SMYD2-ERα and SMYD2-p53 structures provides the first structural insight into the diverse nature of SMYD2 substrate recognition and suggests that the broad specificity of SMYD2 is achieved by multiple molecular mechanisms such as distinct peptide binding modes and the intrinsic dynamics of peptide ligands. Strikingly, a novel potentially SMYD2-specific polyethylene glycol binding site is identified in the CTD domain, implicating possible functions in extended substrate binding or protein-protein interactions. Our study thus provides the structural basis for the SMYD2-mediated ERα methylation, and the resulting knowledge of SMYD2 substrate specificity and target binding diversity could have important implications in selective drug design against a wide range of ERα-related diseases.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N-lysine methyltransferase SMYD2
A
433Homo sapiensMutation(s): 1 
Gene Names: SMYD2 (KMT3C)
EC: 2.1.1.-
Find proteins for Q9NRG4 (Homo sapiens)
Go to Gene View: SMYD2
Go to UniProtKB:  Q9NRG4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Estrogen receptor
B
11Homo sapiensMutation(s): 0 
Gene Names: ESR1 (ESR, NR3A1)
Find proteins for P03372 (Homo sapiens)
Go to Gene View: ESR1
Go to UniProtKB:  P03372
Small Molecules
Ligands 4 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
PE8
Query on PE8

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Download CCD File 
A
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
C16 H34 O9
GLZWNFNQMJAZGY-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

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Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
NI
Query on NI

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Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.822 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.175 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 151.810α = 90.00
b = 151.810β = 90.00
c = 52.873γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXrefinement
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-26
    Type: Initial release
  • Version 1.1: 2014-10-08
    Type: Database references