1GWF

Compound II structure of Micrococcus Lysodeikticus catalase

1GWF の概要

• エントリーDOI: 10.2210/pdb1gwf/pdb
• 関連するPDBエントリー: 1GWE 1GWH
• 分子名称: Catalase, PROTOPORPHYRIN IX CONTAINING FE, SULFATE ION, ... (6 entities in total)
• 機能のキーワード: oxidoreductase, catalase, hydrogen peroxide oxidoreductase
• 由来する生物種: Micrococcus luteus (Micrococcus lysodeikticus)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 58081.35

構造登録者

Murshudov, G.N.,Grebenko, A.I.,Brannigan, J.A.,Antson, A.A.,Barynin, V.V.,Dodson, G.G.,Dauter, Z.,Wilson, K.S.,Melik-Adamyan, W.R. (登録日: 2002-03-15, 公開日: 2002-04-26, 最終更新日: 2025-04-09)

主引用文献

Murshudov, G.N.,Grebenko, A.I.,Brannigan, J.A.,Antson, A.A.,Barynin, V.V.,Dodson, G.G.,Dauter, Z.,Wilson, K.S.,Melik-Adamyan, W.R.
The Structures of Micrococcus Lysodeikticus Catalase, its Ferryl Intermediate (Compound II) and Nadph Complex.
Acta Crystallogr.,Sect.D, 58:1972-1982, 2002

PubMed Abstract: The crystal structure of the bacterial catalase from Micrococcus lysodeikticus has been refined using the gene-derived sequence both at 0.88 A resolution using data recorded at 110 K and at 1.5 A resolution with room-temperature data. The atomic resolution structure has been refined with individual anisotropic atomic thermal parameters. This has revealed the geometry of the haem and surrounding protein, including many of the H atoms, with unprecedented accuracy and has characterized functionally important hydrogen-bond interactions in the active site. The positions of the H atoms are consistent with the enzymatic mechanism previously suggested for beef liver catalase. The structure reveals that a 25 A long channel leading to the haem is filled by partially occupied water molecules, suggesting an inherent facile access to the active site. In addition, the structures of the ferryl intermediate of the catalase, the so-called compound II, at 1.96 A resolution and the catalase complex with NADPH at 1.83 A resolution have been determined. Comparison of compound II and the resting state of the enzyme shows that the binding of the O atom to the iron (bond length 1.87 A) is associated with increased haem bending and is accompanied by a distal movement of the iron and the side chain of the proximal tyrosine. Finally, the structure of the NADPH complex shows that the cofactor is bound to the molecule in an equivalent position to that found in beef liver catalase, but that only the adenine part of NADPH is visible in the present structure.

PubMed: 12454454
DOI: 10.1107/S0907444902016566

実験手法

X-RAY DIFFRACTION (1.96 Å)