Disentangling Unusual Catalytic Properties and the Role of the [4Fe-4S] Cluster of Three Endonuclease III from the Extremophile D. radiodurans

Endonuclease III (EndoIII) is a bifunctional DNA glycosylase with specificity for a broad range of oxidized DNA lesions. The genome of an extremely radiation- and desiccation-resistant bacterium, Deinococcus radiodurans, possesses three genes encoding for EndoIII-like enzymes (DrEndoIII1, DrEndoIII2 and DrEndoIII3), which reveal different types of catalytic activities. DrEndoIII2 acts as the main EndoIII in this organism, while DrEndoIII1 and 3 demonstrate unusual and no EndoIII activity, respectively. In order to understand the role of DrEndoIII1 and DrEndoIII3 in D. radiodurans, we have generated mutants which target non-conserved residues in positions considered essential for classic EndoIII activity. In parallel, we have substituted residues coordinating the iron atoms in the [4Fe-4S] cluster in DrEndoIII2, aiming at elucidating the role of the cluster in these enzymes. Our results demonstrate that the amino acid substitutions in DrEndoIII1 reduce the enzyme activity without altering the overall structure, revealing that the residues found in the wild-type enzyme are essential for its unusual activity. The attempt to generate catalytic activity of DrEndoIII3 by re-designing its catalytic pocket was unsuccessful. A mutation of the iron-coordinating cysteine 199 in DrEndoIII2 appears to compromise the structural integrity and induce the formation of a [3Fe-4S] cluster, but apparently without affecting the activity. Taken together, we provide important structural and mechanistic insights into the three EndoIIIs, which will help us disentangle the open questions related to their presence in D. radiodurans and their particularities.

Noncatalytic Domains in DNA Glycosylases

Many proteins consist of two or more structural domains: separate parts that have a defined structure and function. For example, in enzymes, the catalytic activity is often localized in a core fragment, while other domains or disordered parts of the same protein participate in a number of regulatory processes. This situation is often observed in many DNA glycosylases, the proteins that remove damaged nucleobases thus initiating base excision DNA repair. This review covers the present knowledge about the functions and evolution of such noncatalytic parts in DNA glycosylases, mostly concerned with the human enzymes but also considering some unique members of this group coming from plants and prokaryotes.

Human endonuclease III/NTH1: focusing on the [4Fe–4S] cluster and the N-terminal domain

Full length and truncated human Endonuclease III/hNTH1 possess distinct conformations, redox properties and interactions with the damaged DNA substrate.

Advancing Techniques for Investigating the Enzyme-Electrode Interface

Enzymes are the essential catalytic components of biology and adsorbing redox-active enzymes on electrode surfaces enables the direct probing of their function. Through standard electrochemical measurements, catalytic activity, reversibility and stability, potentials of redox-active cofactors, and interfacial electron transfer rates can be readily measured. Mechanistic investigations on the high electrocatalytic rates and selectivity of enzymes may yield inspiration for the design of synthetic molecular and heterogeneous electrocatalysts. Electrochemical investigations of enzymes also aid in our understanding of their activity within their biological environment and why they evolved in their present structure and function. However, the conventional array of electrochemical techniques (e.g., voltammetry and chronoamperometry) alone offers a limited picture of the enzyme–electrode interface.

How many enzymes are loaded onto an electrode? In which orientation(s) are they bound? What fraction is active, and are single or multilayers formed? Does this static picture change over time, applied voltage, or chemical environment? How does charge transfer through various intraprotein cofactors contribute to the overall performance and catalytic bias? What is the distribution of individual enzyme activities within an ensemble of active protein films? These are central questions for the understanding of the enzyme–electrode interface, and a multidisciplinary approach is required to deliver insightful answers.

Complementing standard electrochemical experiments with an orthogonal set of techniques has recently allowed to provide a more complete picture of enzyme–electrode systems. Within this framework, we first discuss a brief history of achievements and challenges in enzyme electrochemistry. We subsequently describe how the aforementioned challenges can be overcome by applying advanced electrochemical techniques, quartz-crystal microbalance measurements, and spectroscopic, namely, resonance Raman and infrared, analysis. For example, rotating ring disk electrochemistry permits the simultaneous determination of reaction kinetics and quantification of generated products. In addition, recording changes in frequency and dissipation in a quartz crystal microbalance allows to shed light into enzyme loading, relative orientation, clustering, and denaturation at the electrode surface. Resonance Raman spectroscopy yields information on ligation and redox state of enzyme cofactors, whereas infrared spectroscopy provides insights into active site states and the protein secondary and tertiary structure. The development of these emerging methods for the analysis of the enzyme–electrode interface is the primary focus of this Account. We also take a critical look at the remaining gaps in our understanding and challenges lying ahead toward attaining a complete mechanistic picture of the enzyme–electrode interface.

Resonance Raman spectroscopy of Fe-S proteins and their redox properties

Resonance Raman spectra of Fe-S proteins are sensitive to the cluster type, structure and symmetry. Furthermore, bands that originate from bridging and terminal Fe-S vibrations in the 2Fe-2S, 3Fe-4S and 4Fe-4S clusters can be sensitively distinguished in the spectra, as well as the type of non-cysteinyl coordinating ligands, if present. For these reasons, resonance Raman spectroscopy has been playing an exceptionally active role in the studies of Fe-S proteins of diverse structures and functions. We provide here a concise overview of the structural information that can be obtained from resonance Raman spectroscopy on Fe-S clusters, and in parallel, refer to their thermodynamic properties (e.g., reduction potential), which together define the physiological roles of Fe-S proteins. We demonstrate how the knowledge gained over the past several decades on simple clusters nowadays enables studies of complex structures that include Fe-S clusters coupled to other centers and transient processes that involve cluster inter-conversion, biogenesis, disassembly and catalysis.

Spectroelectrochemical insights into structural and redox properties of immobilized endonuclease III and its catalytically inactive mutant

Endonuclease III is a Fe-S containing bifunctional DNA glycosylase which is involved in the repair of oxidation damaged DNA. Here we employ surface enhanced IR spectroelectrochemistry and electrochemistry to study the enzyme from the highly radiation- and desiccation-resistant bacterium Deinococcus radiodurans (DrEndoIII₂). The experiments are designed to shed more light onto specific parameters that are currently proposed to govern damage search and recognition by endonucleases III. We demonstrate that electrostatic interactions required for the redox activation of DrEndoIII₂ may result in high electric fields that alter its structural and thermodynamic properties. Analysis of inactive DrEndoIII₂ (K132A/D150A double mutant) interacting with undamaged DNA, and the active enzyme interacting with damaged DNA also indicate that the electron transfer is modulated by subtle differences in the protein-DNA complex.

Evidence for the synthesis of an unusual high spin (S = 7/2) [Cu–3Fe–4S] cluster in the radical-SAM enzyme RSAD2 (viperin)

We demonstrate the synthesis of an unusual high spin [Cu–3Fe–4S] cluster in the radical S-adenosylmethionine enzyme RSAD2 (also known as viperin).

Electrochemistry of the [4Fe4S] Cluster in Base Excision Repair Proteins: Tuning the Redox Potential with DNA

Escherichia coli endonuclease III (EndoIII) and MutY are DNA glycosylases that contain [4Fe4S] clusters and that serve to maintain the integrity of the genome after oxidative stress. Electrochemical studies on highly oriented pyrolytic graphite (HOPG) revealed that DNA binding by EndoIII leads to a large negative shift in the midpoint potential of the cluster, consistent with stabilization of the oxidized [4Fe4S]3+ form. However, the smooth, hydrophobic HOPG surface is nonideal for working with proteins in the absence of DNA. In this work, we use thin film voltammetry on a pyrolytic graphite edge electrode to overcome these limitations. Improved adsorption leads to substantial signals for both EndoIII and MutY in the absence of DNA, and a large negative potential shift is retained with DNA present. In contrast, the EndoIII mutants E200K, Y205H, and K208E, which provide electrostatic perturbations in the vicinity of the cluster, all show DNA-free potentials within error of wild type; similarly, the presence of negatively charged poly-l-glutamate does not lead to a significant potential shift. Overall, binding to the DNA polyanion is the dominant effect in tuning the redox potential of the [4Fe4S] cluster, helping to explain why all DNA-binding proteins with [4Fe4S] clusters studied to date have similar DNA-bound potentials.

Structural and functional characterization of two unusual endonuclease III enzymes from Deinococcus radiodurans

While most bacteria possess a single gene encoding the bifunctional DNA glycosylase Endonuclease III (EndoIII) in their genomes, Deinococcus radiodurans possesses three: DR2438 (DrEndoIII1), DR0289 (DrEndoIII2) and DR0982 (DrEndoIII3). Here we have determined the crystal structures of DrEndoIII1 and an N-terminally truncated form of DrEndoIII3 (DrEndoIII3Δ76). We have also generated a homology model of DrEndoIII2 and measured activity of the three enzymes. All three structures consist of two all α-helical domains, one of which exhibits a [4Fe-4S] cluster and the other a HhH-motif, separated by a DNA binding cleft, similar to previously determined structures of endonuclease III from Escherichia coli and Geobacillus stearothermophilus. However, both DrEndoIII1 and DrEndoIII3 possess an extended HhH motif with extra helical features and an altered electrostatic surface potential. In addition, the DNA binding cleft of DrEndoIII3 seems to be less accessible for DNA interactions, while in DrEndoIII1 it seems to be more open. Analysis of the enzyme activities shows that DrEndoIII2 is most similar to the previously studied enzymes, while DrEndoIII1 seems to be more distant with a weaker activity towards substrate DNA containing either thymine glycol or an abasic site. DrEndoIII3 is the most distantly related enzyme and displays no detectable activity towards these substrates even though the suggested catalytic residues are conserved. Based on a comparative structural analysis, we suggest that the altered surface potential, shape of the substrate-binding pockets and specific amino acid substitutions close to the active site and in the DNA interacting loops may underlie the unexpected differences in activity.