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Title: Structural basis for the target specificity of actin histidine methyltransferase SETD3

Abstract

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.

Authors:
 [1]; ORCiD logo [1];  [1];  [2];  [1]; ORCiD logo [2]; ORCiD logo [1]
  1. Univ. of Texas MD Anderson Cancer Center, Houston, TX (United States)
  2. Stanford Univ., CA (United States)
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
National Institutes of Health (NIH); Cancer Prevention Research Institute of Texas (CPRIT)
OSTI Identifier:
1571667
Grant/Contract Number:  
R01GM07964; GM11430; RP130397; 1S10OD012304-01; P30CA016672.
Resource Type:
Accepted Manuscript
Journal Name:
Nature Communications
Additional Journal Information:
Journal Volume: 10; Journal Issue: 1; Journal ID: ISSN 2041-1723
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
ENGLISH
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; Enzyme mechanisms; methylation; transferases; x-ray crystallography

Citation Formats

Dai, Shaobo, Horton, John R., Woodcock, Clayton B., Wilkinson, Alex W., Zhang, Xing, Gozani, Or, and Cheng, Xiaodong. Structural basis for the target specificity of actin histidine methyltransferase SETD3. United States: N. p., 2019. Web. https://doi.org/10.1038/s41467-019-11554-6.
Dai, Shaobo, Horton, John R., Woodcock, Clayton B., Wilkinson, Alex W., Zhang, Xing, Gozani, Or, & Cheng, Xiaodong. Structural basis for the target specificity of actin histidine methyltransferase SETD3. United States. https://doi.org/10.1038/s41467-019-11554-6
Dai, Shaobo, Horton, John R., Woodcock, Clayton B., Wilkinson, Alex W., Zhang, Xing, Gozani, Or, and Cheng, Xiaodong. Tue . "Structural basis for the target specificity of actin histidine methyltransferase SETD3". United States. https://doi.org/10.1038/s41467-019-11554-6. https://www.osti.gov/servlets/purl/1571667.
@article{osti_1571667,
title = {Structural basis for the target specificity of actin histidine methyltransferase SETD3},
author = {Dai, Shaobo and Horton, John R. and Woodcock, Clayton B. and Wilkinson, Alex W. and Zhang, Xing and Gozani, Or and Cheng, Xiaodong},
abstractNote = {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.},
doi = {10.1038/s41467-019-11554-6},
journal = {Nature Communications},
number = 1,
volume = 10,
place = {United States},
year = {2019},
month = {8}
}

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Cited by: 4 works
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