5CHR

Dehaloperoxidase B in complex with substrate p-nitrocatechol

Summary for 5CHR

• Entry DOI: 10.2210/pdb5chr/pdb
• Related: 5CHQ
• Descriptor: Dehaloperoxidase B, PROTOPORPHYRIN IX CONTAINING FE, SULFATE ION, ... (7 entities in total)
• Functional Keywords: substrate, oxidoreductase
• Biological source: Amphitrite ornata
• Total number of polymer chains: 2
• Total formula weight: 32872.52

Authors

Carey, L.,Ghiladi, R. (deposition date: 2015-07-10, release date: 2016-04-27, Last modification date: 2024-03-06)

Primary citation

McCombs, N.L.,D'Antonio, J.,Barrios, D.A.,Carey, L.M.,Ghiladi, R.A.
Nonmicrobial Nitrophenol Degradation via Peroxygenase Activity of Dehaloperoxidase-Hemoglobin from Amphitrite ornata.
Biochemistry, 55:2465-2478, 2016

PubMed Abstract: The marine hemoglobin dehaloperoxidase (DHP) from Amphitrite ornata was found to catalyze the H2O2-dependent oxidation of nitrophenols, an unprecedented nonmicrobial degradation pathway for nitrophenols by a hemoglobin. Using 4-nitrophenol (4-NP) as a representative substrate, the major monooxygenated product was 4-nitrocatechol (4-NC). Isotope labeling studies confirmed that the O atom incorporated was derived exclusively from H2O2, indicative of a peroxygenase mechanism for 4-NP oxidation. Accordingly, X-ray crystal structures of 4-NP (1.87 Å) and 4-NC (1.98 Å) bound to DHP revealed a binding site in close proximity to the heme cofactor. Peroxygenase activity could be initiated from either the ferric or oxyferrous states with equivalent substrate conversion and product distribution. The 4-NC product was itself a peroxidase substrate for DHP, leading to the secondary products 5-nitrobenzene-triol and hydroxy-5-nitro-1,2-benzoquinone. DHP was able to react with 2,4-dinitrophenol (2,4-DNP) but was unreactive against 2,4,6-trinitrophenol (2,4,6-TNP). pH dependence studies demonstrated increased reactivity at lower pH for both 4-NP and 2,4-DNP, suggestive of a pH effect that precludes the reaction with 2,4,6-TNP at or near physiological conditions. Stopped-flow UV-visible spectroscopic studies strongly implicate a role for Compound I in the mechanism of 4-NP oxidation. The results demonstrate that there may be a much larger number of nonmicrobial enzymes that are underrepresented when it comes to understanding the degradation of persistent organic pollutants such as nitrophenols in the environment.

PubMed: 27070125
DOI: 10.1021/acs.biochem.6b00143

Experimental method

X-RAY DIFFRACTION (1.98 Å)