5WY0

Crystal structure of the methyltranferase domain of human HEN1 in complex with AdoMet

Summary for 5WY0

• Entry DOI: 10.2210/pdb5wy0/pdb
• Descriptor: Small RNA 2'-O-methyltransferase, S-ADENOSYLMETHIONINE (3 entities in total)
• Functional Keywords: rna methyltranferase, adomet, transferase
• Biological source: Homo sapiens (Human)
• Total number of polymer chains: 1
• Total formula weight: 26520.98

Authors

Peng, L.,Ma, J.B.,Wu, L.G.,Huang, Y. (deposition date: 2017-01-10, release date: 2018-01-17, Last modification date: 2024-03-20)

Primary citation

Peng, L.,Zhang, F.,Shang, R.,Wang, X.,Chen, J.,Chou, J.J.,Ma, J.,Wu, L.,Huang, Y.
Identification of substrates of the small RNA methyltransferase Hen1 in mouse spermatogonial stem cells and analysis of its methyl-transfer domain
J. Biol. Chem., 293:9981-9994, 2018

PubMed Abstract: Small noncoding RNAs (sncRNAs) regulate many genes in eukaryotic cells. Hua enhancer 1 (Hen1) is a 2'--methyltransferase that adds a methyl group to the 2'-OH of the 3'-terminal nucleotide of sncRNAs. The types and properties of sncRNAs may vary among different species, and the domain composition, structure, and function of Hen1 proteins differ accordingly. In mammals, Hen1 specifically methylates sncRNAs called P-element-induced wimpy testis-interacting RNAs (piRNAs). However, other types of sncRNAs that are methylated by Hen1 have not yet been reported, and the structures and the substrates of mammalian Hen1 remain unknown. Here, we report that mouse Hen1 (mHen1) performs 3'-end methylation of classical piRNAs, as well as those of most noncanonical piRNAs derived from rRNAs, small nuclear RNAs and tRNAs in murine spermatogonial stem cells. Moreover, we found that a distinct class of tRNA-derived sncRNAs are mHen1 substrates. We further determined the crystal structure of the putative methyltransferase domain of human Hen1 (HsHen1) in complex with its cofactor AdoMet at 2.0 Å resolution. We observed that HsHen1 has an active site similar to that of plant Hen1. We further found that the putative catalytic domain of HsHen1 alone exhibits no activity. However, an FPP motif at its N terminus conferred full activity to this domain, and additional binding assays suggested that the FPP motif is important for substrate binding. Our findings shed light on its methylation substrates in mouse spermatogonial stem cells and the substrate-recognition mechanism of mammalian Hen1.

PubMed: 29703750
DOI: 10.1074/jbc.RA117.000837

Experimental method

X-RAY DIFFRACTION (2.001 Å)