4FH6

Structure of DHP A in complex with 2,4,6-tribromophenol in 10% DMSO

4FH6 の概要

• エントリーDOI: 10.2210/pdb4fh6/pdb
• 関連するPDBエントリー: 4FH7
• 分子名称: Dehaloperoxidase A, PROTOPORPHYRIN IX CONTAINING FE, SULFATE ION, ... (7 entities in total)
• 機能のキーワード: peroxidase, globin, oxidoreductase
• 由来する生物種: Amphitrite ornata
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 33422.09

構造登録者

de Serrano, V.S.,Franzen, S. (登録日: 2012-06-05, 公開日: 2013-03-27, 最終更新日: 2023-09-13)

主引用文献

Zhao, J.,de Serrano, V.,Zhao, J.,Le, P.,Franzen, S.
Structural and Kinetic Study of an Internal Substrate Binding Site in Dehaloperoxidase-Hemoglobin A from Amphitrite ornata.
Biochemistry, 52:2427-2439, 2013

PubMed Abstract: X-ray crystal structures of dehaloperoxidase-hemoglobin A (DHP A) from Amphitrite ornata soaked with substrate, 2,4,6-tribromophenol (2,4,6-TBP), in buffer solvent with added methanol (MeOH), 2-propanol (2-PrOH), and dimethyl sulfoxide (DMSO) reveal an internal substrate binding site deep in the distal pocket above the α-edge of the heme that is distinct from the previously determined internal inhibitor binding site. The peroxidase function of DHP A has most often been studied using 2,4,6-trichlorophenol (2,4,6-TCP) as a substrate analogue because of the low solubility of 2,4,6-TBP in an aqueous buffer solution. Previous studies at low substrate concentrations pointed to the binding of substrate 2,4,6-TCP at an external site near the exterior heme β- or δ-edge as observed in the class of heme peroxidases. Here we report that the turnover frequencies of both substrates 2,4,6-TCP and 2,4,6-TBP deviate from Michaelis-Menten kinetics at high concentrations. The turnover frequency reaches a maximum in the range of 1400-1700 μM, with a decrease in rate at higher concentrations that is both substrate- and solvent-dependent. The X-ray crystal structure is consistent with the presence of an internal active site above the heme α-edge, in which the substrate would be oxidized in two consecutive steps inside the enzyme, followed by attack by H2O via a water channel in the protein. The physiological role of the internal site may involve interactions with any of a number of aromatic toxins found in benthic ecosystems where A. ornata resides.

PubMed: 23480178
DOI: 10.1021/bi301307f

実験手法

X-RAY DIFFRACTION (1.44 Å)