5H5D

The crystal structure of the yeast arginine methyltransferase SFM1 complexed with MTA

Summary for 5H5D

• Entry DOI: 10.2210/pdb5h5d/pdb
• Related: 5H5E 5H5F
• Descriptor: Protein arginine N-methyltransferase SFM1, 5'-DEOXY-5'-METHYLTHIOADENOSINE (3 entities in total)
• Functional Keywords: arginine methyltransferase, spout fold, transferase
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
• Cellular location: Cytoplasm : Q12314
• Total number of polymer chains: 1
• Total formula weight: 27445.46

Authors

Xie, W.,Wang, C.,Zeng, J. (deposition date: 2016-11-05, release date: 2017-01-18, Last modification date: 2023-11-08)

Primary citation

Wang, C.,Zeng, J.,Xie, W.
A flexible cofactor-binding loop in the novel arginine methyltransferase Sfm1.
FEBS Lett., 591:433-441, 2017

PubMed Abstract: Arginine methylation is a common post-translational modification and is critical for many cellular processes. Sfm1 is a novel arginine methyltransferase that contains a SpoU-TrmD (SPOUT) domain, a typical fold known for RNA methylation, but acts on a ribosomal protein. The underlying mechanism is poorly understood. Here, we report cocrystal structures of Sfm1 in complex with various ligands. We found that a critical loop responsible for S-adenosyl-l-methionine (SAM) binding adopts a different conformation from previous reports, and SAM appears to exhibit double conformations. Deletion of this loop greatly reduces the affinity of Sfm1 to SAM. Additionally, by comparison to closely related tRNA-methyltransferase Trm10, our structural analyses offer a good explanation why the two enzymes utilize distinct substrates, providing insights into the molecular mechanism.

PubMed: 27990635
DOI: 10.1002/1873-3468.12533

Experimental method

X-RAY DIFFRACTION (2.7 Å)