6ICV image
Deposition Date 2018-09-07
Release Date 2019-02-27
Last Version Date 2023-11-22
Entry Detail
PDB ID:
6ICV
Keywords:
Title:
Structure of SETD3 bound to SAH and unmodified actin
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Method Details:
Experimental Method:
Resolution:
2.15 Å
R-Value Free:
0.20
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:Histone-lysine N-methyltransferase setd3
Gene (Uniprot):SETD3
Chain IDs:A, C (auth: B)
Chain Length:504
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Molecule:Actin, cytoplasmic 1
Gene (Uniprot):ACTB
Chain IDs:B (auth: C), D
Chain Length:23
Number of Molecules:2
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Structural insights into SETD3-mediated histidine methylation on beta-actin.
Elife 8 ? ? (2019)
PMID: 30785395 DOI: 10.7554/eLife.43676

Abstact

SETD3 is a member of the SET (Su(var)3-9, Enhancer of zeste, and Trithorax) domain protein superfamily and plays important roles in hypoxic pulmonary hypertension, muscle differentiation, and carcinogenesis. Previously, we identified SETD3 as the actin-specific methyltransferase that methylates the N3 of His73 on β-actin (Kwiatkowski et al., 2018). Here, we present two structures of S-adenosyl-L-homocysteine-bound SETD3 in complex with either an unmodified β-actin peptide or its His-methylated variant. Structural analyses, supported by biochemical experiments and enzyme activity assays, indicate that the recognition and methylation of β-actin by SETD3 are highly sequence specific, and that both SETD3 and β-actin adopt pronounced conformational changes upon binding to each other. In conclusion, this study is the first to show a catalytic mechanism of SETD3-mediated histidine methylation on β-actin, which not only throws light on the protein histidine methylation phenomenon but also facilitates the design of small molecule inhibitors of SETD3.

Legend

Protein

Chemical

Disease

Primary Citation of related structures