2BQZ

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

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

  • DOI: 10.1101/gad.1315905

  • 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 met ...

    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.

    Organizational Affiliation: 

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SET8 PROTEIN
A, E
161Homo sapiensMutation(s): 0 
Gene Names: KMT5A (PRSET7, SET07, SET8, SETD8)
EC: 2.1.1.-
Find proteins for Q9NQR1 (Homo sapiens)
Go to Gene View: KMT5A
Go to UniProtKB:  Q9NQR1
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HISTONE H4
B, F
10Homo sapiensMutation(s): 0 
Gene Names: SMYD5 (RAI15)
EC: 2.1.1.-
Find proteins for Q6GMV2 (Homo sapiens)
Go to Gene View: SMYD5
Go to UniProtKB:  Q6GMV2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SAH
Query on SAH
Download SDF File 
Download CCD File 
A, E
S-ADENOSYL-L-HOMOCYSTEINE
C14 H20 N6 O5 S
ZJUKTBDSGOFHSH-WFMPWKQPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MLZ
Query on MLZ
B, F
L-PEPTIDE LINKINGC7 H16 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.187 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 42.179α = 64.74
b = 46.322β = 86.66
c = 51.998γ = 90.61
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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