4ILZ

Structural and kinetic study of an internal substrate binding site of dehaloperoxidase-hemoglobin A from Amphitrite ornata

Summary for 4ILZ

• Entry DOI: 10.2210/pdb4ilz/pdb
• Related: 4FH6 4FH7
• Descriptor: Dehaloperoxidase A, PROTOPORPHYRIN IX CONTAINING FE, SULFATE ION, ... (7 entities in total)
• Functional Keywords: peroxidase, globin, oxidoreductase
• Biological source: Amphitrite ornata
• Total number of polymer chains: 2
• Total formula weight: 33497.88

Authors

de Serrano, V.S.,Zhao, J.,Zhao, J.,Franzen, S. (deposition date: 2013-01-01, release date: 2013-03-27, Last modification date: 2023-09-20)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.91 Å)