6OX1

SETD3 in Complex with an Actin Peptide with Target Histidine Partially Methylated


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.949 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for the target specificity of actin histidine methyltransferase SETD3.

Dai, S.Horton, J.R.Woodcock, C.B.Wilkinson, A.W.Zhang, X.Gozani, O.Cheng, X.

(2019) Nat Commun 10: 3541-3541

  • DOI: 10.1038/s41467-019-11554-6
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • SETD3 is an actin histidine-N <sub>3 </sub> methyltransferase, whereas other characterized SET-domain enzymes are protein lysine methyltransferases. We report that in a pre-reactive complex SETD3 binds the N <sub>3 </sub>-protonated form (N <sub>3 </ ...

    SETD3 is an actin histidine-N 3 methyltransferase, whereas other characterized SET-domain enzymes are protein lysine methyltransferases. We report that in a pre-reactive complex SETD3 binds the N 3 -protonated form (N 3 -H) of actin His73, and in a post-reactive product complex, SETD3 generates the methylated histidine in an N 1 -protonated (N 1 -H) and N 3 -methylated form. During the reaction, the imidazole ring of His73 rotates ~105°, which shifts the proton from N 3 to N 1 , thus ensuring that the target atom N 3 is deprotonated prior to the methyl transfer. Under the conditions optimized for lysine deprotonation, SETD3 has weak lysine methylation activity on an actin peptide in which the target His73 is substituted by a lysine. The structure of SETD3 with Lys73-containing peptide reveals a bent conformation of Lys73, with its side chain aliphatic carbons tracing along the edge of imidazole ring and the terminal ε-amino group occupying a position nearly identical to the N 3 atom of unmethylated histidine.


    Related Citations: 
    • SETD3 is an actin histidine methyltransferase that prevents primary dystocia.
      Wilkinson, A.W.,Diep, J.,Dai, S.,Liu, S.,Ooi, Y.S.,Song, D.,Li, T.M.,Horton, J.R.,Zhang, X.,Liu, C.,Trivedi, D.V.,Ruppel, K.M.,Vilches-Moure, J.G.,Casey, K.M.,Mak, J.,Cowan, T.,Elias, J.E.,Nagamine, C.M.,Spudich, J.A.,Cheng, X.,Carette, J.E.,Gozani, O.
      (2019) Nature 565: 372


    Organizational Affiliation

    Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA.,Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA. xcheng5@mdanderson.org.,Department of Biology, Stanford University, Stanford, CA, 94305, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Actin, cytoplasmic 1
Y, Z
15Homo sapiensMutation(s): 0 
Gene Names: ACTB
Find proteins for P60709 (Homo sapiens)
Go to Gene View: ACTB
Go to UniProtKB:  P60709
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase setd3
A, B
599Homo 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
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
SAH
Query on SAH

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.949 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.170 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 60.308α = 90.00
b = 175.865β = 92.38
c = 66.967γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM049245-23

Revision History 

  • Version 1.0: 2019-08-21
    Type: Initial release
  • Version 1.1: 2020-01-01
    Type: Author supporting evidence