3IQF

Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methenyl-tetrahydromethanopterin

3IQF の概要

• エントリーDOI: 10.2210/pdb3iqf/pdb
• 関連するPDBエントリー: 3IQE 3IQZ
• 分子名称: F420-dependent methylenetetrahydromethanopterin dehydrogenase, 1-{4-[(6S,6aR,7R)-3-amino-6,7-dimethyl-1-oxo-1,2,5,6,6a,7-hexahydro-8H-imidazo[1,5-f]pteridin-10-ium-8-yl]phenyl}-1-deoxy-5-O-{5-O-[(S)-{[(1S)-1,3-dicarboxypropyl]oxy}(hydroxy)phosphoryl]-alpha-D-ribofuranosyl}-D-ribitol, CALCIUM ION, ... (5 entities in total)
• 機能のキーワード: binary complex of protein and substrate, methanogenesis, one-carbon metabolism, oxidoreductase
• 由来する生物種: Methanopyrus kandleri
• タンパク質・核酸の鎖数: 12
• 化学式量合計: 386746.38

構造登録者

Ceh, K.E.,Demmer, U.,Warkentin, E.,Moll, J.,Thauer, R.K.,Shima, S.,Ermler, U. (登録日: 2009-08-20, 公開日: 2009-10-06, 最終更新日: 2023-11-01)

主引用文献

Ceh, K.,Demmer, U.,Warkentin, E.,Moll, J.,Thauer, R.K.,Shima, S.,Ermler, U.
Structural basis of the hydride transfer mechanism in F(420)-dependent methylenetetrahydromethanopterin dehydrogenase
Biochemistry, 48:10098-10105, 2009

PubMed Abstract: F(420)-dependent methylenetetrahydromethanopterin (methylene-H(4)MPT) dehydrogenase (Mtd) of Methanopyrus kandleri is an enzyme of the methanogenic energy metabolism that catalyzes the reversible hydride transfer between methenyl-H(4)MPT(+) and methylene-H(4)MPT using coenzyme F(420) as hydride carrier. We determined the structures of the Mtd-methylene-H(4)MPT, Mtd-methenyl-H(4)MPT(+), and the Mtd-methenyl-H(4)MPT(+)-F(420)H(2) complexes at 2.1, 2.0, and 1.8 A resolution, respectively. The pterin-imidazolidine-phenyl ring system is present in a new extended but not planar conformation which is virtually identical in methenyl-H(4)MPT(+) and methylene-H(4)MPT at the current resolution. Both substrates methenyl-H(4)MPT(+) and F(420)H(2) bind in a face to face arrangement to an active site cleft, thereby ensuring a direct hydride transfer between their C14a and C5 atoms, respectively. The polypeptide scaffold does not reveal any significant conformational change upon binding of the bulky substrates but in turn changes the conformations of the substrate rings either to avoid clashes between certain ring atoms or to adjust the rings involved in hydride transfer for providing an optimal catalytic efficiency.

PubMed: 19761261
DOI: 10.1021/bi901104d

実験手法

X-RAY DIFFRACTION (2.1 Å)