6ICT

Structure of SETD3 bound to SAH and methylated actin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.952 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Structural insights into SETD3-mediated histidine methylation on beta-actin.

Guo, Q.Liao, S.Kwiatkowski, S.Tomaka, W.Yu, H.Wu, G.Tu, X.Min, J.Drozak, J.Xu, C.

(2019) Elife 8: --

  • DOI: 10.7554/eLife.43676
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • SETD3 is a member of the SET (Su(var)3-9, Enhancer of zeste, and Trithorax) domain protein superfamily and plays important roles in hypoxic pulmonary hypertension, muscle differentiation, and carcinogenesis. Previously, we identified SETD3 as the act ...

    SETD3 is a member of the SET (Su(var)3-9, Enhancer of zeste, and Trithorax) domain protein superfamily and plays important roles in hypoxic pulmonary hypertension, muscle differentiation, and carcinogenesis. Previously, we identified SETD3 as the actin-specific methyltransferase that methylates the N3 of His73 on β-actin (Kwiatkowski et al., 2018). Here, we present two structures of S -adenosyl-L-homocysteine-bound SETD3 in complex with either an unmodified β-actin peptide or its His-methylated variant. Structural analyses, supported by biochemical experiments and enzyme activity assays, indicate that the recognition and methylation of β-actin by SETD3 are highly sequence specific, and that both SETD3 and β-actin adopt pronounced conformational changes upon binding to each other. In conclusion, this study is the first to show a catalytic mechanism of SETD3-mediated histidine methylation on β-actin, which not only throws light on the protein histidine methylation phenomenon but also facilitates the design of small molecule inhibitors of SETD3.


    Organizational Affiliation

    Department of Physiology, University of Toronto, Toronto, Canada.,Division of Molecular and Cellular Biophysics, Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, China.,Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Warsaw, Poland.,Structural Genomics Consortium, University of Toronto, Toronto, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase setd3
A, B, C, D
504Homo sapiensMutation(s): 0 
Gene Names: SETD3 (C14orf154)
EC: 2.1.1.85
Find proteins for Q86TU7 (Homo sapiens)
Go to Gene View: SETD3
Go to UniProtKB:  Q86TU7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Actin, cytoplasmic 1
E, G, H, I
23Homo sapiensMutation(s): 0 
Gene Names: ACTB
Find proteins for P60709 (Homo sapiens)
Go to Gene View: ACTB
Go to UniProtKB:  P60709
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download SDF File 
Download CCD File 
A, B, C, D
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HIC
Query on HIC
E, G, H, I
L-PEPTIDE LINKINGC7 H11 N3 O2HIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.952 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 59.976α = 90.00
b = 176.693β = 93.37
c = 125.892γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31570737
National Natural Science Foundation of ChinaChina31770806

Revision History 

  • Version 1.0: 2019-02-27
    Type: Initial release
  • Version 2.0: 2019-03-06
    Type: Data collection, Database references, Polymer sequence