3NDI

X-ray Structure of a C-3'-Methyltransferase in Complex with S-adenosylmethionine and dTMP

3NDI の概要

• エントリーDOI: 10.2210/pdb3ndi/pdb
• 関連するPDBエントリー: 3NDJ
• 分子名称: Methyltransferase, S-ADENOSYLMETHIONINE, ZINC ION, ... (6 entities in total)
• 機能のキーワード: s-adenosylmethionine, kijanose, tetronitrose, tetradeoxysugar, micromonospora chalcea, tcab9, c-3'-methyltransferase, sugar methylation, transferase
• 由来する生物種: Micromonospora chalcea
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 47066.91

構造登録者

Bruender, N.A.,Thoden, J.B.,Kaur, M.,Avey, M.K.,Holden, H.M. (登録日: 2010-06-07, 公開日: 2010-06-30, 最終更新日: 2024-04-03)

主引用文献

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

実験手法

X-RAY DIFFRACTION (1.5 Å)