Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 40.29 kDa 
• Atom Count: 3437 
• Modelled Residue Count: 342 
• Deposited Residue Count: 342 
• Unique protein chains: 2

2BQZ

Crystal structure of a ternary complex of the human histone methyltransferase Pr-SET7 (also known as SET8)

• DOI: 10.2210/pdb2BQZ/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-04-28 Released: 2005-06-08 
• Deposition Author(s): Xiao, B., Jing, C., Kelly, G., Walker, P.A., Muskett, F.W., Frenkiel, T.A., Martin, S.R., Sarma, K., Reinberg, D., Gamblin, S.J., Wilson, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.206 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 

Literature

Specificity and Mechanism of the Histone Methyltransferase Pr-Set7

Xiao, B., Jing, C., Kelly, G., Walker, P.A., Muskett, F.W., Frenkiel, T.A., Martin, S.R., Sarma, K., Reinberg, D., Gamblin, S.J., Wilson, J.R.

(2005) Genes Dev 19: 1444

• PubMed: 15933069 
• DOI: 10.1101/gad.1315905
• Primary Citation of Related Structures:  
  2BQZ


• PubMed Abstract: 
  

Methylation of lysine residues of histones is an important epigenetic mark that correlates with functionally distinct regions of chromatin. We present here the crystal structure of a ternary complex of the enzyme Pr-Set7 (also known as Set8) that methylates Lys 20 of histone H4 (H4-K20). We show that the enzyme is exclusively a mono-methylase and is therefore responsible for a signaling role quite distinct from that established by other enzymes that target this histone residue. We provide evidence from NMR for the C-flanking domains of SET proteins becoming ordered upon addition of AdoMet cofactor and develop a model for the catalytic cycle of these enzymes. The crystal structure reveals the basis of the specificity of the enzyme for H4-K20 because a histidine residue within the substrate, close to the target lysine, is required for completion of the active site. We also show how a highly variable component of the SET domain is responsible for many of the enzymes' interactions with its target histone peptide and probably also how this part of the structure ensures that Pr-Set7 is nucleosome specific.

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Organizational Affiliation: 

National Institute for Medical Research, The Ridgeway, Mill Hill, London, NW7 1AA, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SET8 PROTEIN	A, E	161	Homo sapiens	Mutation(s): 0  Gene Names: KMT5A, PRSET7, SET07, SET8, SETD8 EC: 2.1.1.43 (PDB Primary Data), 2.1.1 (UniProt), 2.1.1.361 (UniProt)
Find proteins for Q9NQR1 (Homo sapiens) Explore Q9NQR1  Go to UniProtKB:  Q9NQR1
NIH Common Fund Data Resources
PHAROS:  Q9NQR1 GTEx:  ENSG00000183955

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE H4	B, F	10	Homo sapiens	Mutation(s): 0  Gene Names: SMYD5, RAI15 EC: 2.1.1
Find proteins for Q6GMV2 (Homo sapiens) Explore Q6GMV2  Go to UniProtKB:  Q6GMV2
NIH Common Fund Data Resources
PHAROS:  Q6GMV2 GTEx:  ENSG00000135632

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.206 
• R-Value Work: 0.187 
• R-Value Observed: 0.188 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.179	α = 64.74
b = 46.322	β = 86.66
c = 51.998	γ = 90.61

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-04-28 
• Released Date: 2005-06-08 
Deposition Author(s): Xiao, B., Jing, C., Kelly, G., Walker, P.A., Muskett, F.W., Frenkiel, T.A., Martin, S.R., Sarma, K., Reinberg, D., Gamblin, S.J., Wilson, J.R.

Revision History  

• Version 1.0: 2005-06-08
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance