3I58

Crystal structure of an O-methyltransferase (NcsB1) from neocarzinostatin biosynthesis in complex with S-adenosyl-L-homocysteine (SAH) and 2-hydroxy-7-methoxy-5-methyl naphthoic acid (NA)

Summary for 3I58

• Entry DOI: 10.2210/pdb3i58/pdb
• Related: 3I53 3I5U 3I64
• Descriptor: O-methyltransferase, S-ADENOSYL-L-HOMOCYSTEINE, 2-hydroxy-7-methoxy-5-methyl naphthoic acid, ... (5 entities in total)
• Functional Keywords: ternary complex, rossmann-like fold, methyltransferase, transferase
• Biological source: Streptomyces carzinostaticus subsp. neocarzinostaticus
• Total number of polymer chains: 2
• Total formula weight: 70683.68

Authors

Cooke, H.A.,Bruner, S.D. (deposition date: 2009-07-03, release date: 2009-09-01, Last modification date: 2023-09-06)

Primary citation

Cooke, H.A.,Guenther, E.L.,Luo, Y.,Shen, B.,Bruner, S.D.
Molecular basis of substrate promiscuity for the SAM-dependent O-methyltransferase NcsB1, involved in the biosynthesis of the enediyne antitumor antibiotic neocarzinostatin.
Biochemistry, 48:9590-9598, 2009

PubMed Abstract: The small molecule component of chromoprotein enediyne antitumor antibiotics is biosynthesized through a convergent route, incorporating amino acid, polyketide, and carbohydrate building blocks around a central enediyne hydrocarbon core. The naphthoic acid moiety of the enediyne neocarzinostatin plays key roles in the biological activity of the natural product by interacting with both the carrier protein and duplex DNA at the site of action. We have previously described the in vitro characterization of an S-adenosylmethionine-dependent O-methyltransferase (NcsB1) in the neocarzinostatin biosynthetic pathway [Luo, Y., Lin, S., Zhang, J., Cooke, H. A., Bruner, S. D., and Shen, B. (2008) J. Biol. Chem. 283, 14694-14702]. Here we provide a structural basis for NcsB1 activity, illustrating that the enzyme shares an overall architecture with a large family of S-adenosylmethionine-dependent proteins. In addition, NcsB1 represents the first enzyme to be structurally characterized in the biosynthetic pathway of neocarzinostatin. By cocrystallizing the enzyme with various combinations of the cofactor and substrate analogues, details of the active site structure have been established. Changes in subdomain orientation were observed via comparison of structures in the presence and absence of substrate, suggesting that reorientation of the enzyme is involved in binding of the substrate. In addition, residues important for substrate discrimination were predicted and probed through site-directed mutagenesis and in vitro biochemical characterization.

PubMed: 19702337
DOI: 10.1021/bi901257q

Experimental method

X-RAY DIFFRACTION (2.69 Å)