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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 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 boun ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase, H3 lysine-4 specific SET7A261Homo sapiensMutation(s): 0 
Gene Names: SET7KIAA1717SETD7KMT7SET9
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.364 (UniProt)
Find proteins for Q8WTS6 (Homo sapiens)
Explore Q8WTS6 
Go to UniProtKB:  Q8WTS6
NIH Common Fund Data Resources
PHAROS  Q8WTS6
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TAF10 peptide, Acetyl-Ser-Lys-Ser-Mlz-Asp-Arg-Lys-Tyr-Thr-LeuB11N/AMutation(s): 0 
Find proteins for Q12962 (Homo sapiens)
Explore Q12962 
Go to UniProtKB:  Q12962
NIH Common Fund Data Resources
PHAROS  Q12962
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH

Download CCD File 
A
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLZ
Query on MLZ
BL-PEPTIDE LINKINGC7 H16 N2 O2LYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SAHIC50:  30000   nM  BindingDB
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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