2F69

Ternary complex of SET7/9 bound to AdoHcy and a TAF10 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structural basis for the methylation site specificity of SET7/9

Couture, J.-F.Collazo, E.Hauk, G.Trievel, R.C.

(2006) Nat Struct Mol Biol 13: 140-146

  • DOI: https://doi.org/10.1038/nsmb1045
  • Primary Citation of Related Structures:  
    2F69

  • PubMed Abstract: 

    Human SET7/9 is a protein lysine methyltransferase (PKMT) that methylates histone H3, the tumor suppressor p53 and the TBP-associated factor TAF10. To elucidate the determinants of its substrate specificity, we have solved the enzyme's structure bound to a TAF10 peptide and examined its ability to methylate histone H3, TAF10 and p53 substrates bearing either mutations or covalent modifications within their respective methylation sites. Collectively, our data reveal that SET7/9 recognizes a conserved K/R-S/T/A motif preceding the lysine substrate and has a propensity to bind aspartates and asparagines on the C-terminal side of the lysine target. We then used a sequence-based approach with this motif to identify novel substrates for this PKMT. Among the putative targets is TAF7, which is methylated at Lys5 by the enzyme in vitro. These results demonstrate the predictive value of the consensus motif in identifying novel substrates for SET7/9.


  • Organizational Affiliation

    Department of Biological Chemistry, University of Michigan, 1301 Catherine Road, Ann Arbor, Michigan 48109-0606, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-4 specific SET7261Homo sapiensMutation(s): 0 
Gene Names: SET7KIAA1717
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.364 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WTS6 (Homo sapiens)
Explore Q8WTS6 
Go to UniProtKB:  Q8WTS6
PHAROS:  Q8WTS6
GTEx:  ENSG00000145391 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WTS6
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TAF10 peptide, Acetyl-Ser-Lys-Ser-Mlz-Asp-Arg-Lys-Tyr-Thr-Leu11N/AMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q12962 (Homo sapiens)
Explore Q12962 
Go to UniProtKB:  Q12962
PHAROS:  Q12962
GTEx:  ENSG00000166337 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12962
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download Ideal Coordinates CCD File 
C [auth A]S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLZ
Query on MLZ
B
L-PEPTIDE LINKINGC7 H16 N2 O2LYS
Binding Affinity Annotations 
IDSourceBinding Affinity
SAH BindingDB:  2F69 IC50: min: 3.00e+4, max: 4.70e+4 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.38α = 90
b = 83.38β = 90
c = 95.52γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-17
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description