7V6L

LcCOMT in complex with SAH

Summary for 7V6L

• Entry DOI: 10.2210/pdb7v6l/pdb
• Descriptor: LcCOMT, S-ADENOSYL-L-HOMOCYSTEINE (3 entities in total)
• Functional Keywords: transferase, sam, complex
• Biological source: Ligusticum chuanxiong
• Total number of polymer chains: 2
• Total formula weight: 80677.17

Authors

Yu, Y.,CHen, Q. (deposition date: 2021-08-20, release date: 2021-12-29, Last modification date: 2023-11-29)

Primary citation

Song, S.,Chen, A.,Zhu, J.,Yan, Z.,An, Q.,Zhou, J.,Liao, H.,Yu, Y.
Structure basis of the caffeic acid O-methyltransferase from Ligusiticum chuanxiong to understand its selective mechanism.
Int.J.Biol.Macromol., 194:317-330, 2022

PubMed Abstract: Caffeic acid O-methyltransferase from Ligusticum chuanxiong (LcCOMT) showed strict regiospecificity despite a relative degree of preference. Compared with caffeic acid, methyl caffeate was the preferential substrate by its low Km and high Kcat. In this study, we obtained the SAM binary (1.80 Å) and SAH binary (1.95 Å) complex LcCOMT crystal structures, and established the ternary complex structure with methyl caffeate by molecular docking. The active site of LcCOMT included phenolic substrate pocket, SAM/SAH ligand pocket and conserved catalytic residues as well. The regiospecificity of LcCOMT that permitted only 3-hydroxyl group to be methylated arise from the interactions between the active site and the phenyl ring. However, the propanoid tail governed the relative preference of LcCOMT. The ester group in methyl caffeate stabilized the anionic intermediate caused by His268-Asp269 pair, whereas caffeic acid was unable to stabilize the anionic intermediate due to the adjacent carboxylate anion in the propanoid tail. Ser183 residue formed an additional hydrogen bond with SAH and its role was identified by S183A mutation. Ile318 residue might be a potential site for determination of substrate preference, and its mutation led to the change of tertiary conformation. The results supported the selective mechanism of LcCOMT.

PubMed: 34838855
DOI: 10.1016/j.ijbiomac.2021.11.135

Experimental method

X-RAY DIFFRACTION (1.948 Å)