Introduction

Background

(PDB: 8H7C) is a de novo ferric enterobactin esterase designed to highlight the potential of synthetic biology in creating simpler protein structures capable of performing complex functions ^[1]. Syn-F4 is also the first de novo protein catalytically active in vitro and biologically functional in vivo ^[1]. Ferric enterobactin esterases are a type of endogenous bacterial enzyme that break ester bonds of small metabolites bound to iron, allowing iron to be released into and utilized by bacterial cells ^{[2] [3]}. Iron plays crucial roles in various physiological processes in bacteria, including cellular respiration, oxidative stress responses, and DNA and protein synthesis ^[3].

Fes is one such native esterase responsible for releasing Fe³⁺ from iron-chelating compounds, such as ferric enterobactin, within the cell, making it critical for bacterial survival ^{[2] [4]}. In order to mimic evolutionary selection of proteins for specific biological functions, Syn-IF was a de novo bifunctional protein designed to perform iron release, similar to Fes. Syn-IF was subjected to a series of random mutagenesis to individually select for its iron-releasing function, leading to the creation of Syn-F4 ^[5]. While Syn-F4 catalysis is 1000-fold slower than that of a native Fes enzyme, it is still sufficient in rescuing function in ∆fes E.coli ^{[1] [5]}.

Whereas most ferric enterobactin esterases are serine hydrolases that function via a catalytic triad, such as Fes, Syn-F4 performs its function via a catalytic dyad without the involvement of a serine active site residue ^{[1] [4]}. One other serine hydrolase, IroE, also performs catalysis through a catalytic dyad but still uses a serine residue as the nucleophile ^{[6] [4]}. The unassuming design of Syn-F4 was modeled after the de novo protein WA20, the crystallization of which revealed an , which served as the basis for the design of Syn-F4 ^{[7] [1]}.

Ligand

Ferric enterobactin is a metabolite that is part of a larger family of siderophores, which are low-molecular-weight, high-affinity, iron-chelating compounds that facilitate the transport of iron across the cell membrane ^{[2] [3]}. (PDB: 2XUZ) is characterized by three catecholamine groups linked together by a trilactone ring and an exceptionally high affinity for Fe³⁺ (K = 1052 M⁻¹) ^{[2] [8]}. It is easily degraded when not bound to iron, which is coordinated to ferric enterobactin by six hydroxyl groups and released by the hydrolysis of an ester bond ^{[2] [8]}.

Structure

Figure 1. Unresolved residues of "loop left" structure.

Alpha-Helix Bundle

The crystallization of the de novo protein, (PDB: 3VJF), revealed an alpha-helix bundle structure, which served as the foundation for the design of Syn-F4 ^[7]. While structurally similar, Syn-F4 features a novel active site characterized by the presence of a ^[1]. Despite its simple appearance, the structure is highly coordinated and efficient due to this active site. The symmetry of the four-helix bundle, combined with the configuration of the central hole, facilitates catalytic activity by effectively cleaving the ester bond in ferric enterobactin ^[1].

Stabilizing Factors

The on either side of the bundles significantly contribute to the stability of Syn-F4. Due to the symmetry of the chains, both chain A and chain B display the same residues and are linked by unresolved residues (Fig. 1) ^[1]. The accumulated negative charge on the C-termini is stabilized by positively-charged residues (H10, H45, H46, R102), and conversely, the accumulated positive charge on the N-termini is stabilized by negatively-charged residues (D59). Additionally, the within the core of Syn-F4 interact via Van der Waals to promote association between the helices.

The orientation of the alpha helices and their associated interactions could not be definitively determined due to the absence of loop residues in the crystallized structure of Syn-F4 ^[1]. To address this, molecular dynamics (MD) simulations were performed to estimate the predominant conformation of the helices ^[1]. Two potential conformations were identified: "loop left" and "loop right" ^[1]. Among these, the "loop left" conformation demonstrated greater stability and was therefore considered the preferred structure (Fig. 1) ^[1].

Function

Figure 2. The scissile bond of ferric enterobactin is denoted by a dotted line, and the electrophile is indicated by the arrow.

Active Site

The of Syn-F4 lies within the central hole of the structure, made up of five catalytic residues (E26, H74, R77, K78, and H85) that facilitate binding to ferric enterobactin and catalyze hydrolysis of the scissile (ester) bond, which is indicated by the dotted line (Fig. 2) ^[1]. The mutation of any of these five resides completely abrogates the function of the enzyme ^[1].

Mechanism

The mechanism of Syn-F4 was proposed to function at pH 6.0 via a catalytic dyad with histidine (H74) and glutamate (E26) residues and water attacking as the nucleophile ^[1]. The electrophile is an oxygen making up one of the ester bonds of the ligand, denoted by an arrow (Fig. 2). A representation of the possible mechanism of Syn-F4 performing hydrolysis of the scissile bond of ferric enterobactin follows:

Step 1

A potential first step of the Syn-F4 mechanism involves the activation of water as the nucleophile (Fig. 3). E26 first de-protonates H74, which then de-protonates H2O in turn (Fig. 3).

Figure 3. Activation of water as the nucleophile.

Step 2

A potential second step of the Syn-F4 mechanism involves two transition states. The first transition state is characterized by the nucleophile attacking the electrophile, kicking electron density up onto the carboxyl group, whereas the second transition state is characterized by the electron density on the carboxyl group collapsing and kicking off the leaving group (Fig. 4).

Figure 4. Two transition states.

Step 3

A potential third step of the Syn-F4 mechanism shows the release of Fe³⁺ as the ferric enterobactin structure linearizes (Fig. 5). The enzyme is reset by the re-protonation of H74 by E26 (Fig. 5).

Figure 5. Release of iron and resetting the enzyme.

Related Structures

Both the structure and mechanism of Syn-F4 differ from other native ferric enterobactin esterases whose structures have been previously determined. Native (isolated from S. flexneri, PDB: 3C87) and (isolated from E. coli, PDB: 2GZR) enzymes are both serine hydrolases, which means a serine residue acts as their nucleophile ^{[6] [4] [9]}. Native Fes acts via a catalytic triad (E345, H375, and S281), whereas IroE acts via a catalytic dyad (H287 and S189), similar to Syn-F4 ^{[6] [4] [9]}.

Relevance

Synthetic Biology

Synthetic biology, and specifically de novo proteins, are at the forefront of biochemical industrial applications in an effort to mimic evolutionary selection of proteins for specific functions. These designed proteins may be further useful in developing improved antibiotic therapies and novel treatments for cancer ^{[10] [11] [12] [13]}.