2B0J

The crystal structure of the apoenzyme of the iron-sulfur-cluster-free hydrogenase (Hmd)

2B0J の概要

• エントリーDOI: 10.2210/pdb2b0j/pdb
• 分子名称: 5,10-methenyltetrahydromethanopterin hydrogenase (2 entities in total)
• 機能のキーワード: rossmann fold, helix bundle, oxidoreductase
• 由来する生物種: Methanocaldococcus jannaschii
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 38739.07

構造登録者

Pilak, O.,Mamat, B.,Vogt, S.,Hagemeier, C.H.,Thauer, R.K.,Shima, S.,Vonrhein, C.,Warkentin, E.,Ermler, U. (登録日: 2005-09-14, 公開日: 2006-04-18, 最終更新日: 2024-04-03)

主引用文献

Pilak, O.,Mamat, B.,Vogt, S.,Hagemeier, C.H.,Thauer, R.K.,Shima, S.,Vonrhein, C.,Warkentin, E.,Ermler, U.
The Crystal Structure of the Apoenzyme of the Iron-Sulphur Cluster-free Hydrogenase
J.Mol.Biol., 358:798-809, 2006

PubMed Abstract: The iron-sulphur cluster-free hydrogenase (Hmd, EC 1.12.98.2) from methanogenic archaea is a novel type of hydrogenase that tightly binds an iron-containing cofactor. The iron is coordinated by two CO molecules, one sulphur and a pyridone derivative, which is linked via a phosphodiester bond to a guanosine base. We report here on the crystal structure of the Hmd apoenzyme from Methanocaldococcus jannaschii at 1.75 A and from Methanopyrus kandleri at 2.4 A resolution. Homodimeric Hmd reveals a unique architecture composed of one central and two identical peripheral globular units. The central unit is composed of the intertwined C-terminal segments of both subunits, forming a novel intersubunit fold. The two peripheral units consist of the N-terminal domain of each subunit. The Rossmann fold-like structure of the N-terminal domain contains a mononucleotide-binding site, which could harbour the GMP moiety of the cofactor. Another binding site for the iron-containing cofactor is most probably Cys176, which is located at the bottom of a deep intersubunit cleft and which has been shown to be essential for enzyme activity. Adjacent to the iron of the cofactor modelled as a ligand to Cys176, an extended U-shaped extra electron density, interpreted as a polyethyleneglycol fragment, suggests a binding site for the substrate methenyltetrahydromethanopterin.

PubMed: 16540118
DOI: 10.1016/j.jmb.2006.02.035

実験手法

X-RAY DIFFRACTION (1.75 Å)