8IA9 image
Entry Detail
PDB ID:
8IA9
Keywords:
Title:
SpnK Methyltransferase from the Spinosyn Biosynthetic Pathway in Complex with Mg
Biological Source:
Source Organism:
PDB Version:
Deposition Date:
2023-02-08
Release Date:
2023-09-27
Method Details:
Experimental Method:
Resolution:
2.50 Å
R-Value Free:
0.24
R-Value Work:
0.20
R-Value Observed:
0.20
Space Group:
P 43 21 2
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Demethylmacrocin O-methyltransferase
Chain IDs:A, B
Chain Length:397
Number of Molecules:2
Biological Source:Saccharopolyspora spinosa
Ligand Molecules
Primary Citation
Structural and computational insights into the regioselectivity of SpnK involved in rhamnose methylation of spinosyn.
Int.J.Biol.Macromol. 253 126763 126763 (2023)
PMID: 37703985 DOI: 10.1016/j.ijbiomac.2023.126763

Abstact

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.

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Primary Citation of related structures