› 3f9w

X-ray diffraction
1.6Å resolution

Structural Insights into Lysine Multiple Methylation by SET Domain Methyltransferases, SET8-Y334F / H4-Lys20 / AdoHcy

Released:
DOI: 10.2210/pdb3f9w/pdb
PDB entry 3f9w coloured by chain, front view.
PDB entry 3f9w coloured by chain, side view.
PDB entry 3f9w coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural origins for the product specificity of SET domain protein methyltransferases.
Couture JF, Dirk LM, Brunzelle JS, Houtz RL, Trievel RC
Proc Natl Acad Sci U S A 105 20659-64 (2008)
PMID: 19088188

Function and Biology Details

Reaction catalysed: 
S-adenosyl-L-methionine + a [histone H4]-L-lysine(20) = S-adenosyl-L-homocysteine + a [histone H4]-N(6)-methyl-L-lysine(20)
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158688 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
N-lysine methyltransferase KMT5A Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 166 amino acids
Theoretical weight: 18.77 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21
UniProt:
  • Canonical: Q9NQR1 (Residues: 232-393; Coverage: 41%)
Gene names: KMT5A, PRSET7, SET07, SET8, SETD8
Sequence domains: SET domain
Structure domains: SET domain
Histone H4 Chains: E, F, G, H
Molecule details ›
Chains: E, F, G, H
Length: 10 amino acids
Theoretical weight: 1.28 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P62805 (Residues: 16-25; Coverage: 10%)
Gene names: H4-16, H4/A, H4/B, H4/C, H4/D, H4/E, H4/G, H4/H, H4/I, H4/J, H4/K, H4/M, H4/N, H4/O, H4C1, H4C11, H4C12, H4C13, H4C14, H4C15, H4C16, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4F2, H4FA, H4FB, H4FC, H4FD, H4FE, H4FG, H4FH, H4FI, H4FJ, H4FK, H4FM, H4FN, H4FO, HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4, HIST2H4A, HIST2H4B, HIST4H4

Ligands and Environments

1 bound ligand:
Ligand SAH 4 x SAH
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P1
Unit cell:
a: 44Å b: 45.6Å c: 94.2Å
α: 89.2° β: 87.1° γ: 90.8°
R-values:
R R work R free
0.164 0.162 0.206
Expression systems:
  • Escherichia coli BL21
  • Not provided

Quick links

Citations

12 review citations

Carbon-oxygen hydrogen bonding in biological structure and function.
Horowitz et al. (2012)
11 more

9 mentions without citation

Chemical and Biochemical Perspectives of Protein Lysine Methylation.
Luo M. (2018)
8 more