3NDJ

X-ray Structure of a C-3'-Methyltransferase in Complex with S-Adenosyl-L-Homocysteine and Sugar Product

Summary for 3NDJ

• Entry DOI: 10.2210/pdb3ndj/pdb
• Related: 3NDI
• Descriptor: Methyltransferase, S-ADENOSYL-L-HOMOCYSTEINE, ZINC ION, ... (6 entities in total)
• Functional Keywords: s-adenosyl-l-homocysteine, kijanose, tetronitrose, tetradeoxy sugar, keto sugar, micromonospora chalcea, tcab9, c-3'-methyltransferase, sugar methylation, transferase
• Biological source: Micromonospora chalcea
• Total number of polymer chains: 1
• Total formula weight: 47179.06

Authors

Bruender, N.A.,Thoden, J.B.,Kaur, M.,Avey, M.K.,Holden, H.M. (deposition date: 2010-06-07, release date: 2010-06-30, Last modification date: 2024-04-03)

Primary citation

Bruender, N.A.,Thoden, J.B.,Kaur, M.,Avey, M.K.,Holden, H.M.
Molecular Architecture of a C-3'-Methyltransferase Involved in the Biosynthesis of d-Tetronitrose.
Biochemistry, 49:5891-5898, 2010

PubMed Abstract: S-Adenosylmethionine (SAM)-dependent methyltransferases are involved in a myriad of biological processes, including signal transduction, chromatin repair, metabolism, and biosyntheses, among others. Here we report the high-resolution structure of a novel C-3'-methyltransferase involved in the production of D-tetronitrose, an unusual sugar found attached to the antitumor agent tetrocarcin A or the antibiotic kijanimicin. Specifically, this enzyme, referred to as TcaB9 and cloned from Micromonospora chalcea, catalyzes the conversion of dTDP-3-amino-2,3,6-trideoxy-4-keto-D-glucose to dTDP-3-amino-2,3,6-trideoxy-4-keto-3-methyl-D-glucose. For this analysis, two structures were determined to 1.5 A resolution: one in which the enzyme was crystallized in the presence of SAM and dTMP and the other with the protein complexed to S-adenosylhomocysteine and its dTDP-linked sugar product. The overall fold of the monomeric enzyme can be described in terms of three domains. The N-terminal domain harbors the binding site for a zinc ion that is ligated by four cysteines. The middle domain adopts the canonical "SAM-binding" fold with a seven-stranded mixed beta-sheet flanked on either side by three alpha-helices. This domain is responsible for anchoring the SAM cofactor to the protein. Strikingly, the C-terminal domain also contains a seven-stranded beta-sheet, and it appears to be related to the middle domain by an approximate 2-fold rotational axis, thus suggesting TcaB9 arose via gene duplication. Key residues involved in sugar binding include His 181, Glu 224, His 225, and Tyr 222. Their possible roles in catalysis are discussed.

PubMed: 20527922
DOI: 10.1021/bi100782b

Experimental method

X-RAY DIFFRACTION (1.5 Å)