Troxidoreductase, a protein of unknown function found in Archaeoglobus fulgidus shows EC 1 and EC 3 characteristics
Abstract
Troxidoreductase, a protein of unknown function found in Archaeglobus fulgidus, is commonly found in and believed to be responsible for the souring of oil fields via sulfur production. With a hypothesized EC 3 function we tested structure and function by using structural comparison (Pymol/Promol) and ligand binding analysis (Autodock) to examine similarities with proteins of known function and BLASTP and Pfam to search for families and genetic sequence similarities in the DNA. Results showed active site similarities between Troxidoreductase and some EC 3 proteins, but closes structural and ligand binding similarities with EC 1 proteins, leading to the hypothesis that Troxidoreductase is an Oxidoreductase that also has function of a Hydrolase, which could explain the souring of oil fields through the production of sulfur gas when water is present.
Introduction
Oil production is currently a vital industry, as many of the machines used every day around the world are powered by oil-based fuel. Thus, the efficient usage, but also efficient production, of oil cannot be understated, as an oil field turning sour can cost the producers and the customer money, as well endangering workers through the production of sulfur gas. Oil fields are an extreme environment in which few organisms can be found. Those surviving there are often considered extremophiles as they are also found exclusively in extreme conditions, such as on the ocean floor around hydrothermal vents. One such organism able to survive in these conditions is Archaeoglobus fulgidus, a sulfur-loving extremophile. This archaebacteria has been found in the depths of the biosphere, but also in hot deep oil reserves, and is hypothesized to cause the missing first step of hydrocarbon oxidization in oil fields, which then in turn leads to the souring of said oil field or reservoir (Khelifi et al. 2014).
Archaeglobus fulgidus has been found to create a biofilm in response to stressors in the environment which may help it attach to metal in order to stimulate growth in a metal deficient environment, thus aiding in growth as it is a metal-reducing organism (Lapaglia and Hartzell 1997). As a hyper thermophilic sulfur reducing organism, there is reason to believe that A. fulgidus may be the first step of hydrocarbon oxidization in oil fields, which in turn leads to the souring of oil fields and reservoirs (Khelifi et al. 2014). The souring of oil fields leads to increased oil prices to the average consumer, as a high sulfide concentration can lead to rejection by the oil refiners, lowering the supply of oil in the market. It also produces hydrosulfide gas, an extremely toxic gas that lowers air quality and must be monitored during the oil mining process. Furthermore, it can corrode the infrastructure of an oil mining machine and plug the reservoir through the precipitation of iron sulfide, all increasing the cost of the production of oil (Gieg, Jack, & Foght 2011).
In an effort to examine this possible reaction, we have chosen to examine hypothetical binding site Troxidoreductase on hypothetical protein AF_1432. AF_1432 is part of the HD superfamily of metal dependent phosphorylases and a hypothetical protein believed to be found in Archaeglobus fulgidus (Aravind and Koonin 1998). HD domains have been found to play a role in antiviral defense in the human protein SAMHD1 (Beloglazova et al. 2013). The SAMHD1 protein was found to limit replication of the HIV-1 genome, but not HIV-2, and the purified HD domain from humans and mice contained dGTP-stimulated tryptophohydralayse activity (Beloglazova et al. 2013). Troxidoreductase’s enzyme consortium number is 3.1.3.89 where each number separated by periods signifies something about the protein. The 3. Signifies the enzyme is a hydrolase, and the 1 signifies it is an esterase, so it acts on ester bonds. 3.1.3 signifies phosphoric-monoester hydrolases, and the 3.1.3.89 specifies that Troxidoreductase shows specificity towards deoxyribonucleoside 5'-monophosphates (“ENZYME - 3.1.3.89 5’-Deoxynucleotidase.”)
From this information, there is reason to believe the Archaeglobus fulgidus may cause the vital missing step of the souring of oil fields. Due to the organism of origin, as well as the EC number, we hypothesize that Troxidoreductase will have characteristics of a metal dependent phosphorylase due to its origin in A. fulgidus but perform some sort of role of a hydrolase due to its EC 3 classification.