Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 61.73 kDa 
• Atom Count: 4771 
• Residue Count: 512 
• Unique protein chains: 2

1XQH

Crystal structure of a ternary complex of the methyltransferase SET9 (also known as SET7/9) with a P53 peptide and SAH

• DOI: 10.2210/pdb1XQH/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-10-12 Released: 2004-11-23 
• Deposition Author(s): Chuikov, S., Kurash, J.K., Wilson, J.R., Xiao, B., Justin, N., Ivanov, G.S., McKinney, K., Tempst, P., Prives, C., Gamblin, S.J., Barlev, N.A., Reinberg, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.223 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 

Literature

Regulation of p53 activity through lysine methylation

Chuikov, S., Kurash, J.K., Wilson, J.R., Xiao, B., Justin, N., Ivanov, G.S., McKinney, K., Tempst, P., Prives, C., Gamblin, S.J., Barlev, N.A., Reinberg, D.

(2004) Nature 432: 353-360

• PubMed: 15525938 
• DOI: 10.1038/nature03117
• Structures With Same Primary Citation


• PubMed Abstract: 
  

p53 is a tumour suppressor that regulates the cellular response to genotoxic stresses. p53 is a short-lived protein and its activity is regulated mostly by stabilization via different post-translational modifications. Here we report a novel mechanism of p53 regulation through lysine methylation by Set9 methyltransferase. Set9 specifically methylates p53 at one residue within the carboxyl-terminus regulatory region. Methylated p53 is restricted to the nucleus and the modification positively affects its stability. Set9 regulates the expression of p53 target genes in a manner dependent on the p53-methylation site. The crystal structure of a ternary complex of Set9 with a p53 peptide and the cofactor product S-adenosyl-l-homocysteine (AdoHcy) provides the molecular basis for recognition of p53 by this lysine methyltransferase.

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Organizational Affiliation: 

Howard Hughes Medical Institute, Division of Nucleic Acids Enzymology, Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Histone-lysine N-methyltransferase, H3 lysine-4 specific	A, E	264	Homo sapiens	Mutation(s): 0  Gene Names: SETD7, KIAA1717, KMT7, SET7, SET9 EC: 2.1.1.43 (PDB Primary Data), 2.1.1 (UniProt)
Find proteins for Q8WTS6 (Homo sapiens) Go to UniProtKB:  Q8WTS6
NIH Common Fund Data Resources
PHAROS  Q8WTS6 GTEx  ENSG00000145391

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
9-mer peptide from tumor protein p53	B, F	10	N/A	Mutation(s): 1
Find proteins for P04637 (Homo sapiens) Go to UniProtKB:  P04637
NIH Common Fund Data Resources
PHAROS  P04637 GTEx  ENSG00000141510

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAH	A, E	S-ADENOSYL-L-HOMOCYSTEINE C14 H20 N6 O5 S ZJUKTBDSGOFHSH-WFMPWKQPSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLZ	B,F	L-PEPTIDE LINKING	C7 H16 N2 O2		LYS

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
SAH	IC50:  30000   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.223 
• R-Value Work: 0.184 
• R-Value Observed: 0.186 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.374	α = 90
b = 103.123	β = 90.04
c = 67.165	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-10-12 
• Released Date: 2004-11-23 
Deposition Author(s): Chuikov, S., Kurash, J.K., Wilson, J.R., Xiao, B., Justin, N., Ivanov, G.S., McKinney, K., Tempst, P., Prives, C., Gamblin, S.J., Barlev, N.A., Reinberg, D.

Revision History 

• Version 1.0: 2004-11-23
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance