9CKC

Crystal structure of SMYD2 in complex with two PARP1 peptides

9CKC の概要

• エントリーDOI: 10.2210/pdb9ckc/pdb
• 関連するPDBエントリー: 6N3G
• 分子名称: N-lysine methyltransferase SMYD2, Poly [ADP-ribose] polymerase 1, processed C-terminus, S-ADENOSYL-L-HOMOCYSTEINE, ... (5 entities in total)
• 機能のキーワード: smyd2, parp1, methyltransferase, set and mynd-containing protein, transferase
• 由来する生物種: Homo sapiens (human); 詳細
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 106276.25

構造登録者

Zhang, Y.,Alshammari, E.,Spellmon, N.,Brunzelle, J.,Yang, Z. (登録日: 2024-07-08, 公開日: 2025-01-15)

主引用文献

Zhang, Y.,Alshammari, E.,Sobota, J.,Spellmon, N.,Perry, E.,Cao, T.,Mugunamalwaththa, T.,Smith, S.,Brunzelle, J.,Wu, G.,Stemmler, T.,Jin, J.,Li, C.,Yang, Z.
Structure of the SMYD2-PARP1 Complex Reveals Both Productive and Allosteric Modes of Peptide Binding.
Biorxiv, 2024

PubMed Abstract: Allosteric regulation allows proteins to dynamically respond to environmental cues by modulating activity at sites away from the catalytic center. Despite its importance, the SET-domain protein lysine methyltransferase superfamily has been understudied. Here, we present four crystal structures of SMYD2, a unique family member with a MYND domain. Our findings reveal a novel allosteric binding site with high conformational plasticity and promiscuity, capable of binding peptides, proteins, PEG, and small molecules. This site exhibits positive cooperativity with substrate binding, influencing catalytic activity. Mutations here significantly alter substrate affinity, changing the enzyme's kinetic profile. Specificity studies show interaction with PARP1 but not histones, suggesting targeted regulation. Interestingly, this site's function remains unaffected by active site changes, indicating unidirectional mechanisms. Our discovery provides novel insights into SMYD2's biochemical regulation and lays the foundation for broader research on allosteric control in lysine methyltransferases. Given SMYD2's role in various cancers, this work opens exciting avenues for designing specific allosteric inhibitors with reduced off-target effects.

PubMed: 39677743
DOI: 10.1101/2024.12.03.626679

実験手法

X-RAY DIFFRACTION (2.1 Å)