Characterization of SETD3 methyltransferase–mediated protein methionine methylation
Abstract
Most characterized protein methylation events encompass arginine and lysine N-methylation, and only a few cases of protein methionine thiomethylation have been reported. Newly discovered oncohistone mutations include lysine-to-methionine substitutions at positions 27 and 36 of histone H3.3. In these cases, the methionine substitution localizes to the active-site pocket of the corresponding histone lysine methyltransferase, thereby inhibiting the respective transmethylation activity. SET domain–containing 3 (SETD3) is a protein (i.e. actin) histidine methyltransferase. Here, we generated an actin variant in which the histidine target of SETD3 was substituted with methionine. As for previously characterized histone SET domain proteins, the methionine substitution substantially (76-fold) increased binding affinity for SETD3 and inhibited SETD3 activity on histidine. Unexpectedly, SETD3 was active on the substituted methionine, generating S-methylmethionine in the context of actin peptide. The ternary structure of SETD3 in complex with the methionine-containing actin peptide at 1.9 Å resolution revealed that the hydrophobic thioether side chain is packed by the aromatic rings of Tyr312 and Trp273, as well as the hydrocarbon side chain of Ile310. Our results suggest that placing methionine properly in the active site—within close proximity to and in line with the incoming methyl group of SAM—would allow some SET domain proteins tomore »
- Authors:
-
[2];
[1]
- Univ. of Texas, Houston, TX (United States)
- Baylor College of Medicine, Houston, TX (United States)
- Emory Univ., Atlanta, GA (United States)
- Stanford Univ., CA (United States)
- Publication Date:
- Research Org.:
- Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1669126
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Biological Chemistry
- Additional Journal Information:
- Journal Volume: 295; Journal Issue: 32; Journal ID: ISSN 0021-9258
- Publisher:
- American Society for Biochemistry and Molecular Biology
- Country of Publication:
- United States
- Language:
- ENGLISH
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; protein methylation; S-adenosylmethionine (SAM); methionine; protein structure; enzyme catalysis; actin; methionine methylation; methyltransferases S-methylmethionine; SETD3
Citation Formats
Dai, Shaobo, Holt, Matthew V., Horton, John R., Woodcock, Clayton B., Patel, Anamika, Zhang, Xing, Young, Nicolas L., Wilkinson, Alex W., and Cheng, Xiaodong. Characterization of SETD3 methyltransferase–mediated protein methionine methylation. United States: N. p., 2020.
Web. doi:10.1074/jbc.ra120.014072.
Dai, Shaobo, Holt, Matthew V., Horton, John R., Woodcock, Clayton B., Patel, Anamika, Zhang, Xing, Young, Nicolas L., Wilkinson, Alex W., & Cheng, Xiaodong. Characterization of SETD3 methyltransferase–mediated protein methionine methylation. United States. https://doi.org/10.1074/jbc.ra120.014072
Dai, Shaobo, Holt, Matthew V., Horton, John R., Woodcock, Clayton B., Patel, Anamika, Zhang, Xing, Young, Nicolas L., Wilkinson, Alex W., and Cheng, Xiaodong. Fri .
"Characterization of SETD3 methyltransferase–mediated protein methionine methylation". United States. https://doi.org/10.1074/jbc.ra120.014072. https://www.osti.gov/servlets/purl/1669126.
@article{osti_1669126,
title = {Characterization of SETD3 methyltransferase–mediated protein methionine methylation},
author = {Dai, Shaobo and Holt, Matthew V. and Horton, John R. and Woodcock, Clayton B. and Patel, Anamika and Zhang, Xing and Young, Nicolas L. and Wilkinson, Alex W. and Cheng, Xiaodong},
abstractNote = {Most characterized protein methylation events encompass arginine and lysine N-methylation, and only a few cases of protein methionine thiomethylation have been reported. Newly discovered oncohistone mutations include lysine-to-methionine substitutions at positions 27 and 36 of histone H3.3. In these cases, the methionine substitution localizes to the active-site pocket of the corresponding histone lysine methyltransferase, thereby inhibiting the respective transmethylation activity. SET domain–containing 3 (SETD3) is a protein (i.e. actin) histidine methyltransferase. Here, we generated an actin variant in which the histidine target of SETD3 was substituted with methionine. As for previously characterized histone SET domain proteins, the methionine substitution substantially (76-fold) increased binding affinity for SETD3 and inhibited SETD3 activity on histidine. Unexpectedly, SETD3 was active on the substituted methionine, generating S-methylmethionine in the context of actin peptide. The ternary structure of SETD3 in complex with the methionine-containing actin peptide at 1.9 Å resolution revealed that the hydrophobic thioether side chain is packed by the aromatic rings of Tyr312 and Trp273, as well as the hydrocarbon side chain of Ile310. Our results suggest that placing methionine properly in the active site—within close proximity to and in line with the incoming methyl group of SAM—would allow some SET domain proteins to selectively methylate methionine in proteins.},
doi = {10.1074/jbc.ra120.014072},
journal = {Journal of Biological Chemistry},
number = 32,
volume = 295,
place = {United States},
year = {2020},
month = {6}
}
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