6M81

Crystal structure of TylM1 Y14F bound to SAH and dTDP-phenol

Summary for 6M81

• Entry DOI: 10.2210/pdb6m81/pdb
• Descriptor: dTDP-3-amino-3,6-dideoxy-alpha-D-glucopyranose N,N-dimethyltransferase, S-ADENOSYL-L-HOMOCYSTEINE, 5'-O-[(S)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]thymidine, ... (4 entities in total)
• Functional Keywords: tylm1, n-methyltransferase, transferase
• Biological source: Streptomyces fradiae
• Total number of polymer chains: 4
• Total formula weight: 117538.30

Authors

Fick, R.J.,McDole, B.G.,Trievel, R.C. (deposition date: 2018-08-21, release date: 2019-03-13, Last modification date: 2024-03-13)

Primary citation

Fick, R.J.,Horowitz, S.,McDole, B.G.,Clay, M.C.,Mehl, R.A.,Al-Hashimi, H.M.,Scheiner, S.,Trievel, R.C.
Structural and Functional Characterization of Sulfonium Carbon-Oxygen Hydrogen Bonding in the Deoxyamino Sugar Methyltransferase TylM1.
Biochemistry, 58:2152-2159, 2019

PubMed Abstract: The N-methyltransferase TylM1 from Streptomyces fradiae catalyzes the final step in the biosynthesis of the deoxyamino sugar mycaminose, a substituent of the antibiotic tylosin. The high-resolution crystal structure of TylM1 bound to the methyl donor S-adenosylmethionine (AdoMet) illustrates a network of carbon-oxygen (CH···O) hydrogen bonds between the substrate's sulfonium cation and residues within the active site. These interactions include hydrogen bonds between the methyl and methylene groups of the AdoMet sulfonium cation and the hydroxyl groups of Tyr14 and Ser120 in the enzyme. To examine the functions of these interactions, we generated Tyr14 to phenylalanine (Y14F) and Ser120 to alanine (S120A) mutations to selectively ablate the CH···O hydrogen bonding to AdoMet. The TylM1 S120A mutant exhibited a modest decrease in its catalytic efficiency relative to that of the wild type (WT) enzyme, whereas the Y14F mutation resulted in an approximately 30-fold decrease in catalytic efficiency. In contrast, site-specific substitution of Tyr14 by the noncanonical amino acid p-aminophenylalanine partially restored activity comparable to that of the WT enzyme. Correlatively, quantum mechanical calculations of the activation barrier energies of WT TylM1 and the Tyr14 mutants suggest that substitutions that abrogate hydrogen bonding with the AdoMet methyl group impair methyl transfer. Together, these results offer insights into roles of CH···O hydrogen bonding in modulating the catalytic efficiency of TylM1.

PubMed: 30810306
DOI: 10.1021/acs.biochem.8b01141

Experimental method

X-RAY DIFFRACTION (1.782 Å)