8IAA

SpnK Methyltransferase from the Spinosyn Biosynthetic Pathway in Complex with SAH

Summary for 8IAA

• Entry DOI: 10.2210/pdb8iaa/pdb
• Descriptor: Demethylmacrocin O-methyltransferase, S-ADENOSYL-L-HOMOCYSTEINE, MAGNESIUM ION, ... (4 entities in total)
• Functional Keywords: methyltransferase, transferase
• Biological source: Saccharopolyspora spinosa
• Total number of polymer chains: 2
• Total formula weight: 87842.83

Authors

Huang, S.,Zheng, J. (deposition date: 2023-02-08, release date: 2023-09-27)

Primary citation

Huang, S.,Ji, H.,Zheng, J.
Structural and computational insights into the regioselectivity of SpnK involved in rhamnose methylation of spinosyn.
Int.J.Biol.Macromol., 253:126763-126763, 2023

PubMed Abstract: Rhamnose methylation of spinosyn critical for insecticidal activity is orchestrated by substrate specificity of three S-adenosyl-L-methionine (SAM) dependent methyltransferases (MTs). Previous in vitro enzymatic assays indicate that 3'-O-MT SpnK accepts the rhamnosylated aglycone (RAGL) and 2'-O-methylated RAGL as substrates, but does not tolerate the presence of a methoxy moiety at the O-4' position of the rhamnose unit. Here we solved the crystal structures of apo and ligand-bound SpnK, and used molecular dynamic (MD) simulations to decipher the molecular basis of substrate specificity. SpnK assembles into a tetramer, with each set of three monomers forming an integrated substrate binding pocket. The MD simulations of SpnK complexed with RAGL or 2'-O-methylated RAGL revealed that the 4'-hydroxyl of the rhamnose unit formed a hydrogen bond with a conserved Asp299 of the catalytic center, which is disrupted in structures of SpnK complexed with 4'-O-methylated RAGL or 2',4'-di-O-methylated RAGL. Comparison with SpnI methylating the C2'-hydroxyl of RAGL reveals a correlation between a DLQT/DLWT motif and the selectivity of rhamnose O-MTs. Together, our structural and computational results revealed the structural basis of substrate specificity of rhamnose O-MTs and would potentially help the engineering of spinosyn derivatives.

PubMed: 37703985
DOI: 10.1016/j.ijbiomac.2023.126763

Experimental method

X-RAY DIFFRACTION (2.1 Å)