Structural basis for Sfm1 functioning as a protein arginine methyltransferase.

Area of Science:

• Biochemistry
• Structural Biology
• Molecular Biology

Background:

• SPOUT proteins are methyltransferases primarily active on RNAs.
• Yeast Sfm1 was predicted to have a SPOUT domain but its substrate was unknown.
• Previous studies suggested Sfm1 might methylate ribosomal protein S3.

Purpose of the Study:

• To determine the structure and function of yeast Sfm1.
• To elucidate the mechanism by which Sfm1 methylates its substrate.
• To investigate whether Sfm1 acts on RNA or protein.

Main Methods:

• X-ray crystallography to obtain the Sfm1 structure.
• Biochemical assays to test Sfm1 activity towards RNA and ribosomal protein S3.
• Site-directed mutagenesis to assess the role of the C-terminal domain.

Main Results:

• The crystal structure of Sfm1 revealed a typical SPOUT domain and a C-terminal domain.
• Sfm1's active site resembles that of protein arginine methyltransferases (PRMTs) and is unsuitable for RNA binding.
• Biochemical data confirmed Sfm1's high activity towards ribosomal protein S3, specifically methylating Arg146, with no detectable RNA methyltransferase activity.
• The C-terminal domain was found to be critical for substrate binding and Sfm1 activity.

Conclusions:

• Sfm1 functions as a protein arginine methyltransferase (PRMT) for ribosomal protein S3, not an RNA methyltransferase.
• The study provides the structural basis for Sfm1's specific methylation of ribosomal protein S3.
• The findings clarify the substrate specificity and enzymatic mechanism of Sfm1.