6OX3 image
Entry Detail
PDB ID:
6OX3
Keywords:
Title:
SETD3 in Complex with an Actin Peptide with His73 Replaced with Lysine
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2019-05-13
Release Date:
2019-08-21
Method Details:
Experimental Method:
Resolution:
1.79 Å
R-Value Free:
0.24
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 1 21 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Histone-lysine N-methyltransferase setd3
Chain IDs:B (auth: A), D (auth: B)
Chain Length:599
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Actin Peptide
Chain IDs:A (auth: Y), C (auth: Z)
Chain Length:19
Number of Molecules:2
Biological Source:Homo sapiens
Primary Citation

Abstact

SETD3 is an actin histidine-N3 methyltransferase, whereas other characterized SET-domain enzymes are protein lysine methyltransferases. We report that in a pre-reactive complex SETD3 binds the N3-protonated form (N3-H) of actin His73, and in a post-reactive product complex, SETD3 generates the methylated histidine in an N1-protonated (N1-H) and N3-methylated form. During the reaction, the imidazole ring of His73 rotates ~105°, which shifts the proton from N3 to N1, thus ensuring that the target atom N3 is deprotonated prior to the methyl transfer. Under the conditions optimized for lysine deprotonation, SETD3 has weak lysine methylation activity on an actin peptide in which the target His73 is substituted by a lysine. The structure of SETD3 with Lys73-containing peptide reveals a bent conformation of Lys73, with its side chain aliphatic carbons tracing along the edge of imidazole ring and the terminal ε-amino group occupying a position nearly identical to the N3 atom of unmethylated histidine.

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Primary Citation of related structures