4OBX

Crystal structure of yeast Coq5 in the apo form

4OBX の概要

• エントリーDOI: 10.2210/pdb4obx/pdb
• 関連するPDBエントリー: 4OBW
• 分子名称: 2-methoxy-6-polyprenyl-1,4-benzoquinol methylase, mitochondrial, TRIS(HYDROXYETHYL)AMINOMETHANE (3 entities in total)
• 機能のキーワード: rossmann fold, methyltransferase, transferase
• 由来する生物種: Saccharomyces cerevisiae (Baker's yeast)
• 細胞内の位置: Mitochondrion: P49017
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 117335.26

構造登録者

Dai, Y.N.,Zhou, K.,Cao, D.D.,Jiang, Y.L.,Meng, F.,Chi, C.B.,Ren, Y.M.,Chen, Y.X.,Zhou, C.Z. (登録日: 2014-01-07, 公開日: 2014-08-06, 最終更新日: 2023-09-20)

主引用文献

Dai, Y.N.,Zhou, K.,Cao, D.D.,Jiang, Y.L.,Meng, F.,Chi, C.B.,Ren, Y.M.,Chen, Y.,Zhou, C.Z.
Crystal structures and catalytic mechanism of the C-methyltransferase Coq5 provide insights into a key step of the yeast coenzyme Q synthesis pathway.
Acta Crystallogr.,Sect.D, 70:2085-2092, 2014

PubMed Abstract: Saccharomyces cerevisiae Coq5 is an S-adenosyl methionine (SAM)-dependent methyltransferase (SAM-MTase) that catalyzes the only C-methylation step in the coenzyme Q (CoQ) biosynthesis pathway, in which 2-methoxy-6-polyprenyl-1,4-benzoquinone (DDMQH2) is converted to 2-methoxy-5-methyl-6-polyprenyl-1,4-benzoquinone (DMQH2). Crystal structures of Coq5 were determined in the apo form (Coq5-apo) at 2.2 Å resolution and in the SAM-bound form (Coq5-SAM) at 2.4 Å resolution, representing the first pair of structures for the yeast CoQ biosynthetic enzymes. Coq5 displays a typical class I SAM-MTase structure with two minor variations beyond the core domain, both of which are considered to participate in dimerization and/or substrate recognition. Slight conformational changes at the active-site pocket were observed upon binding of SAM. Structure-based computational simulation using an analogue of DDMQH2 enabled us to identify the binding pocket and entrance tunnel of the substrate. Multiple-sequence alignment showed that the residues contributing to the dimeric interface and the SAM- and DDMQH2-binding sites are highly conserved in Coq5 and homologues from diverse species. A putative catalytic mechanism of Coq5 was proposed in which Arg201 acts as a general base to initiate catalysis with the help of a water molecule.

PubMed: 25084328
DOI: 10.1107/S1399004714011559

実験手法

X-RAY DIFFRACTION (2.2 Å)