9WIV
SbSOMT in complex with SAH
Summary for 9WIV
| Entry DOI | 10.2210/pdb9wiv/pdb |
| Descriptor | O-methyltransferase domain-containing protein, S-ADENOSYL-L-HOMOCYSTEINE (3 entities in total) |
| Functional Keywords | methyltransferase, plant o-methyltransferase, complex, transferase |
| Biological source | Sorghum bicolor (Sorghum, Sorghum vulgare) |
| Total number of polymer chains | 2 |
| Total formula weight | 83573.52 |
| Authors | |
| Primary citation | Pow, K.C.,Zhang, N.,Yan, M.,Wang, X.,Lui, A.C.W.,Lo, C.,Hao, Q. Structural dynamics of the pi-stacking network governing cofactor-substrate cooperativity of SbSOMT methyltransferase. Commun Chem, 2026 Cited by PubMed Abstract: SAM-dependent methyltransferases are enzymes that catalyze the transfer of a methyl group from a cofactor to a substrate through an ordered or random sequential bi-bi mechanism. However, the structural dynamics governing binding cooperativity between the cofactor and substrate remain understudied. In this study, we demonstrate that SbSOMT, a plant O-methyltransferase, exhibits bilateral positive cooperativity between the cofactor and substrate, except the unproductive SbSOMT-SAM-pterostilbene complex. Furthermore, SbSOMT displayed substrate-binding kinetics that shift in response to the nature of bound-cofactor. Sinefungin-bound SbSOMT exhibited positive cooperativity primarily attributed to an increased substrate association rate constant (k), whereas SAH-bound SbSOMT displayed positive cooperativity driven primarily by a decreased dissociation rate constant (k). Structural analysis implies that these cooperativity switch and divergent binding kinetics stem from the interactions between the cofactor and substrate at the methyl binding site. Integrating structural insights reveals that a dynamic W279 π-stacking network governs this cooperativity. Upon binding of the first ligand, H196, W279, and H282 rearrange to form a π-stacking network, in which W279 serves as the essential central plane that also stacks with the substrate. Accordingly, W279A mutagenesis substantially impaired the substrate affinity, cooperativity and enzymatic activity. PubMed: 42259925DOI: 10.1038/s42004-026-02087-3 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.9 Å) |
Structure validation
No wwPDB Validation report is currently available for this entry.
