human lysine methyltransferase Smyd3 in complex with AdoHcy (Form III)

Experimental Data Snapshot

  • Resolution: 3.41 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 

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Structural and biochemical studies of human lysine methyltransferase Smyd3 reveal the important functional roles of its post-SET and TPR domains and the regulation of its activity by DNA binding.

Xu, S.Wu, J.Sun, B.Zhong, C.Ding, J.

(2011) Nucleic Acids Res 39: 4438-4449

  • DOI: https://doi.org/10.1093/nar/gkr019
  • Primary Citation of Related Structures:  
    3OXF, 3OXG, 3OXL

  • PubMed Abstract: 

    The SET- and MYND-domain containing (Smyd) proteins constitute a special subfamily of the SET-containing lysine methyltransferases. Here we present the structure of full-length human Smyd3 in complex with S-adenosyl-L-homocysteine at 2.8 Å resolution. Smyd3 affords the first example that other region(s) besides the SET domain and its flanking regions participate in the formation of the active site. Structural analysis shows that the previously uncharacterized C-terminal domain of Smyd3 contains a tetratrico-peptide repeat (TPR) domain which together with the SET and post-SET domains forms a deep, narrow substrate binding pocket. Our data demonstrate the important roles of both TPR and post-SET domains in the histone lysine methyltransferase (HKMT) activity of Smyd3, and show that the hydroxyl group of Tyr239 is critical for the enzymatic activity. The characteristic MYND domain is located nearby to the substrate binding pocket and exhibits a largely positively charged surface. Further biochemical assays show that DNA binding of Smyd3 can stimulate its HKMT activity and the process may be mediated via the MYND domain through direct DNA binding.

  • Organizational Affiliation

    State Key Laboratory of Molecular Biology and Research Center for Structural Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Graduate School of Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai 200031, China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SET and MYND domain-containing protein 3464Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H7B4 (Homo sapiens)
Explore Q9H7B4 
Go to UniProtKB:  Q9H7B4
GTEx:  ENSG00000185420 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H7B4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 3.41 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.225 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.439α = 90
b = 103.439β = 90
c = 112.202γ = 120
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description