6MBK

SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, First P212121 Crystal Form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 372-376

  • DOI: 10.1038/s41586-018-0821-8
  • Primary Citation of Related Structures:  
  • Also Cited By: 6OX5, 6OX4, 6OX3, 6OX2, 6OX1, 6OX0

  • PubMed Abstract: 
  • For more than 50¬†years, the methylation of mammalian actin at histidine 73 has been known to occur <sup>1 </sup>. Despite the pervasiveness of His73 methylation, which we find is conserved in several model animals and plants, its function remains unc ...

    For more than 50 years, the methylation of mammalian actin at histidine 73 has been known to occur 1 . Despite the pervasiveness of His73 methylation, which we find is conserved in several model animals and plants, its function remains unclear and the enzyme that generates this modification is unknown. Here we identify SET domain protein 3 (SETD3) as the physiological actin His73 methyltransferase. Structural studies reveal that an extensive network of interactions clamps the actin peptide onto the surface of SETD3 to orient His73 correctly within the catalytic pocket and to facilitate methyl transfer. His73 methylation reduces the nucleotide-exchange rate on actin monomers and modestly accelerates the assembly of actin filaments. Mice that lack SETD3 show complete loss of actin His73 methylation in several tissues, and quantitative proteomics analysis shows that actin His73 methylation is the only detectable physiological substrate of SETD3. SETD3-deficient female mice have severely decreased litter sizes owing to primary maternal dystocia that is refractory to ecbolic induction agents. Furthermore, depletion of SETD3 impairs signal-induced contraction in primary human uterine smooth muscle cells. Together, our results identify a mammalian histidine methyltransferase and uncover a pivotal role for SETD3 and actin His73 methylation in the regulation of smooth muscle contractility. Our data also support the broader hypothesis that protein histidine methylation acts as a common regulatory mechanism.


    Organizational Affiliation

    Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.,Stanford Healthcare, Palo Alto, CA, USA.,Department of Biology, Stanford University, Stanford, CA, USA.,Department of Comparative Medicine, Stanford University School of Medicine, Stanford, CA, USA.,Department of Biology, Stanford University, Stanford, CA, USA. ogozani@stanford.edu.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA. xcheng5@mdanderson.org.,Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA. carette@stanford.edu.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Actin peptide
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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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

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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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.69 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.228 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.279α = 90.00
b = 115.970β = 90.00
c = 173.589γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing

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 SciencesUnited StatesGM049245-23

Revision History 

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2019-01-16
    Type: Data collection, Database references
  • Version 1.2: 2019-11-13
    Type: Database references