1TW2

Crystal structure of Carminomycin-4-O-methyltransferase (DnrK) in complex with S-adenosyl-L-homocystein (SAH) and 4-methoxy-e-rhodomycin T (M-ET)

Summary for 1TW2

• Entry DOI: 10.2210/pdb1tw2/pdb
• Related: 1QZZ 1R00 1TW3
• Descriptor: Carminomycin 4-O-methyltransferase, S-ADENOSYL-L-HOMOCYSTEINE, METHYL (4R)-2-ETHYL-2,5,12-TRIHYDROXY-7-METHOXY-6,11-DIOXO-4-{[2,3,6-TRIDEOXY-3-(DIMETHYLAMINO)-BETA-D-RIBO-HEXOPYRANOSYL]OXY}-1H,2H,3H,4H,6H,11H-TETRACENE-1-CARBOXYLATE, ... (4 entities in total)
• Functional Keywords: anthracycline, methyltransferase, methylate, streptomyces, tailoring enzyme, polyketide, s-adenosyl-l-homocystein, structural proteomics in europe, spine, structural genomics, transferase
• Biological source: Streptomyces peucetius
• Total number of polymer chains: 2
• Total formula weight: 80248.64

Authors

Jansson, A.,Koskiniemi, H.,Mantsala, P.,Niemi, J.,Schneider, G.,Structural Proteomics in Europe (SPINE) (deposition date: 2004-06-30, release date: 2004-09-14, Last modification date: 2024-04-03)

Primary citation

Jansson, A.,Koskiniemi, H.,Mantsala, P.,Niemi, J.,Schneider, G.
Crystal structure of a ternary complex of DnrK, a methyltransferase in daunorubicin biosynthesis, with bound products
J.Biol.Chem., 279:41149-41156, 2004

PubMed Abstract: One of the final steps in the biosynthesis of the widely used anti-tumor drug daunorubicin in Streptomyces peucetius is the methylation of the 4-hydroxyl group of the tetracyclic ring system. This reaction is catalyzed by the S-adenosyl-L-methionine-dependent carminomycin 4-O-methyltransferase DnrK. The crystal structure of the ternary complex of this enzyme with the bound products S-adenosyl-L-homocysteine and 4-methoxy-epsilon-rhodomycin T has been determined to a 2.35-angstroms resolution. DnrK is a homodimer, and the subunit displays the typical fold of small molecule O-methyltransferases. The structure provides insights into the recognition of the anthracycline substrate and also suggests conformational changes as part of the catalytic cycle of the enzyme. The position and orientation of the bound ligands are consistent with an SN2 mechanism of methyl transfer. Mutagenesis experiments on a putative catalytic base confirm that DnrK most likely acts as an entropic enzyme in that rate enhancement is mainly due to orientational and proximity effects. This contrasts the mechanism of DnrK with that of other O-methyltransferases where acid/base catalysis has been demonstrated to be an essential contribution to rate enhancement.

PubMed: 15273252
DOI: 10.1074/jbc.M407081200

Experimental method

X-RAY DIFFRACTION (2.5 Å)