bioloGPT: What is the role of iron in the active site of Rieske oxygenase

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Quick Answer

Iron in Rieske oxygenases is crucial for electron transfer and dioxygen activation, facilitating the oxidation of substrates into dihydrodiols.

Long Answer

Role of Iron in the Active Site of Rieske Oxygenase

Rieske oxygenases are a class of non-heme iron enzymes that play a vital role in the oxidative degradation of aromatic compounds. The active site of these enzymes typically contains a mononuclear iron atom coordinated by specific amino acid residues, which is essential for their catalytic activity.

1. Coordination and Structure

The iron atom in the active site is usually coordinated by a 2-His-1-carboxylate facial triad, which consists of two histidine residues and one carboxylate group from an aspartate or glutamate. This arrangement allows for a highly reactive environment that facilitates the binding of dioxygen (O₂) and the substrate. The iron is often in a reduced state (Fe²⁺) during the catalytic cycle, which is crucial for its ability to activate O₂ for subsequent reactions.

2. Redox State and Electron Transfer

The redox state of the iron is tightly coupled with the Rieske iron-sulfur cluster, which is involved in electron transfer processes. For instance, in naphthalene dioxygenase (NDO), the Rieske cluster donates electrons to the active site iron, allowing it to reduce O₂ and form reactive iron-oxo species that can oxidize the aromatic substrate into a cis-dihydrodiol product. This process is dependent on the iron being in a reduced state, highlighting the importance of iron's redox properties in the catalytic mechanism.

3. Catalytic Mechanism

During the catalytic cycle, the iron atom binds O₂ in a side-on fashion, which is critical for the stereospecific oxidation of the substrate. The binding of O₂ to the iron facilitates the formation of a peroxo intermediate, which can then undergo further reactions to cleave the O–O bond and generate reactive species that attack the substrate. This mechanism is essential for the dioxygenation reactions catalyzed by Rieske oxygenases.

4. Summary of Key Functions

Electron Transfer: Iron facilitates the transfer of electrons from the Rieske cluster to the active site, enabling the reduction of O₂.
Substrate Activation: The iron's coordination environment allows for the effective binding and activation of substrates for oxidation.
Regulatory Role: The redox state of iron influences the enzyme's activity and substrate specificity, making it a key regulatory element in the catalytic process.

In conclusion, iron plays a multifaceted role in the active site of Rieske oxygenases, acting as a central atom for electron transfer, substrate activation, and the overall catalytic mechanism of dioxygenation.

References

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Updated: January 03, 2025

Key Insight

The unique coordination of iron in Rieske oxygenases not only facilitates substrate oxidation but also plays a critical role in the enzyme's electron transfer mechanisms, highlighting its importance in biocatalysis.

Bioinformatics Wizard

This code analyzes the sequence data of Rieske oxygenases to identify conserved motifs related to iron coordination.

import pandas as pd

# Load sequence data
sequences = pd.read_csv('rieske_sequences.csv')

# Identify conserved motifs
conserved_motifs = sequences[sequences['motif'].str.contains('Fe')]

# Output the conserved motifs
print(conserved_motifs)

Top Search Results

1. Structural Insight into the Dioxygenation of Nitroarene Compounds: the Crystal Structure of Nitrobenzene Dioxygenase [2005]

2. 3-Ketosteroid 9α-hydroxylase enzymes: Rieske non-heme monooxygenases essential for bacterial steroid degradation [2014]

3. Rieske business: Structure–function of Rieske non-heme oxygenases [2005]

4. Characterization of 3-Ketosteroid 9α-Hydroxylase, a Rieske Oxygenase in the Cholesterol Degradation Pathway of Mycobacterium tuberculosis [2009]

Potential Hypothesis

Investigating the potential for engineering Rieske oxygenases to enhance their catalytic efficiency for biotechnological applications

Exploring the role of iron in modulating the substrate specificity of Rieske oxygenases through structural variations

Hypothesis Graveyard

The hypothesis that all Rieske oxygenases have identical iron coordination environments is unlikely, as structural studies show variability among different enzymes.

The assumption that iron's role is solely structural is challenged by evidence of its active participation in electron transfer and substrate activation.

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