3CUR

Structure of a double methionine mutant of NI-FE hydrogenase

3CUR の概要

• エントリーDOI: 10.2210/pdb3cur/pdb
• 関連するPDBエントリー: 1FRF 1YQW 1YRQ 3CUS
• 分子名称: Periplasmic [NiFe] hydrogenase small subunit, Periplasmic [NiFe] hydrogenase large subunit, IRON/SULFUR CLUSTER, ... (10 entities in total)
• 機能のキーワード: ni-fe hydrogenase tunnel mutant, iron, iron-sulfur, metal-binding, oxidoreductase, nickel
• 由来する生物種: Desulfovibrio fructosovorans; 詳細
• 細胞内の位置: Periplasm: P18187 P18188
• タンパク質・核酸の鎖数: 6
• 化学式量合計: 268903.80

構造登録者

Volbeda, A. (登録日: 2008-04-17, 公開日: 2008-08-05, 最終更新日: 2024-11-06)

主引用文献

Leroux, F.,Dementin, S.,Burlat, B.,Cournac, L.,Volbeda, A.,Champ, S.,Martin, L.,Guigliarelli, B.,Bertrand, P.,Fontecilla-Camps, J.,Rousset, M.
Experimental approaches to kinetics of gas diffusion in hydrogenase
Proc.Natl.Acad.Sci.Usa, 105:11188-11193, 2008

PubMed Abstract: Hydrogenases, which catalyze H(2) to H(+) conversion as part of the bioenergetic metabolism of many microorganisms, are among the metalloenzymes for which a gas-substrate tunnel has been described by using crystallography and molecular dynamics. However, the correlation between protein structure and gas-diffusion kinetics is unexplored. Here, we introduce two quantitative methods for probing the rates of diffusion within hydrogenases. One uses protein film voltammetry to resolve the kinetics of binding and release of the competitive inhibitor CO; the other is based on interpreting the yield in the isotope exchange assay. We study structurally characterized mutants of a NiFe hydrogenase, and we show that two mutations, which significantly narrow the tunnel near the entrance of the catalytic center, decrease the rates of diffusion of CO and H(2) toward and from the active site by up to 2 orders of magnitude. This proves the existence of a functional channel, which matches the hydrophobic cavity found in the crystal. However, the changes in diffusion rates do not fully correlate with the obstruction induced by the mutation and deduced from the x-ray structures. Our results demonstrate the necessity of measuring diffusion rates and emphasize the role of side-chain dynamics in determining these.

PubMed: 18685111
DOI: 10.1073/pnas.0803689105

実験手法

X-RAY DIFFRACTION (2.4 Å)