9CKG

Crystal structure of SMYD2 active site mutant

Summary for 9CKG

• Entry DOI: 10.2210/pdb9ckg/pdb
• Related: 6N3G
• Descriptor: N-lysine methyltransferase SMYD2, S-ADENOSYL-L-HOMOCYSTEINE, ZINC ION, ... (7 entities in total)
• Functional Keywords: smyd2, parp1, protein lysine-methyltransferase, set and mynd-containing protein, transferase
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 1
• Total formula weight: 50809.27

Authors

Sobota, J.,Zhang, Y.,Spellmon, N.,Perry, E.,Brunzelle, J.,Yang, Z. (deposition date: 2024-07-08, release date: 2025-01-15)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (2.75 Å)