Structural basis for substrate recognition by the human N-terminal methyltransferase 1

Journal Article · Thu Nov 05 00:00:00 EST 2015 · Genes & Development

DOI:https://doi.org/10.1101/gad.270611.115· OSTI ID:1236265

Dong, Cheng ^[1]; Mao, Yunfei ^[2]; Tempel, Wolfram ^[1]; Qin, Su ^[1]; Li, Li ^[1]; Loppnau, Peter ^[1]; Huang, Rong ^[2]; Min, Jinrong ^[3]

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1. Univ. of Toronto, ON (Canada). Structural Genomics Consortium
2. Virginia Commonwealth Univ., Richmond, VA (United States). Dept. of Medicinal Chemistry, Drug Discovery and Development. The Inst. for Structural Biology, Drug Discovery and Development
3. Univ. of Toronto, ON (Canada). Structural Genomics Consortium. Dept. of Physiology

α-N-terminal methylation represents a highly conserved and prevalent post-translational modification, yet its biological function has remained largely speculative. The recent discovery of α-N-terminal methyltransferase 1 (NTMT1) and its physiological substrates propels the elucidation of a general role of α-N-terminal methylation in mediating DNA-binding ability of the modified proteins. The phenotypes, observed from both NTMT1 knockdown in breast cancer cell lines and knockout mouse models, suggest the potential involvement of α-N-terminal methylation in DNA damage response and cancer development. In this study, we report the first crystal structures of human NTMT1 in complex with cofactor S-adenosyl-L-homocysteine (SAH) and six substrate peptides, respectively, and reveal that NTMT1 contains two characteristic structural elements (a β hairpin and an N-terminal extension) that contribute to its substrate specificity. Our complex structures, coupled with mutagenesis, binding, and enzymatic studies, also present the key elements involved in locking the consensus substrate motif XPK (X indicates any residue type other than D/E) into the catalytic pocket for α-N-terminal methylation and explain why NTMT1 prefers an XPK sequence motif. We propose a catalytic mechanism for α-N-terminal methylation. Overall, this study gives us the first glimpse of the molecular mechanism of α-N-terminal methylation and potentially contributes to the advent of therapeutic agents for human diseases associated with deregulated α-N-terminal methylation.

• Research Organization: Univ. of Toronto, ON (Canada); Virginia Commonwealth Univ., Richmond, VA (United States)
• Sponsoring Organization: USDOE Office of Science (SC), Biological and Environmental Research (BER)
• Grant/Contract Number: AC02-06CH11357
• OSTI ID: 1236265
• Journal Information: Genes & Development, Vol. 29, Issue 22; ISSN 0890-9369
• Publisher: Cold Springs Harbor Press
• Country of Publication: United States
• Language: ENGLISH

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
60 APPLIED LIFE SCIENCES
α-N-terminal methylation
methyltransferase
NTMT1
crystal structure