3S8P

Crystal Structure of the SET Domain of Human Histone-Lysine N-Methyltransferase SUV420H1 In Complex With S-Adenosyl-L-Methionine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal structures of the human histone H4K20 methyltransferases SUV420H1 and SUV420H2.

Wu, H.Siarheyeva, A.Zeng, H.Lam, R.Dong, A.Wu, X.H.Li, Y.Schapira, M.Vedadi, M.Min, J.

(2013) FEBS Lett 587: 3859-3868

  • DOI: https://doi.org/10.1016/j.febslet.2013.10.020
  • Primary Citation of Related Structures:  
    3RQ4, 3S8P

  • PubMed Abstract: 

    SUV420H1 and SUV420H2 are two highly homologous enzymes that methylate lysine 20 of histone H4 (H4K20), a mark that has been implicated in transcriptional regulation. In this study, we present the high-resolution crystal structures of human SUV420H1 and SUV420H2 in complex with SAM, and report their substrate specificity. Both methyltransferases have a unique N-terminal domain and Zn-binding post-SET domain, and prefer the monomethylated histone H4K20 as a substrate in vitro. No histone H4K20 trimethylation activity was detected by our radioactivity-based assay for either enzyme, consistent with the presence of a conserved serine residue that forms a hydrogen bond with the target lysine side-chain and limits the methylation level.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase SUV420H1
A, B
273Homo sapiensMutation(s): 0 
Gene Names: CGI-85KMT5BSUV420H1
EC: 2.1.1.43
UniProt & NIH Common Fund Data Resources
Find proteins for Q4FZB7 (Homo sapiens)
Explore Q4FZB7 
Go to UniProtKB:  Q4FZB7
PHAROS:  Q4FZB7
GTEx:  ENSG00000110066 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ4FZB7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.188 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.424α = 100.99
b = 50.134β = 108.05
c = 74.839γ = 89.76
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DMphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MxDCdata 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: 2011-07-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2014-01-15
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description