In Silico Characterization and Homology Modeling of a Cyanobacterial Phosphoenolpyruvate Carboxykinase Enzyme

Abstract

ATP-dependent phosphoenolpyruvate carboxykinase (PEPCK) is a key catabolic enzyme found in various species of bacteria, plants, and yeast. PEPCK may play a role in carbon fixation in aquatic ecosystems consisting of photosynthetic cyanobacteria. RuBisCO-based CO2fixation is prevalent in cyanobacteria through C3intermediates; however, a significant amount of carbon flows into C4acids during cyanobacterial photosynthesis. This indicates that a C4mechanism for inorganic carbon fixation is prevalent in cyanobacteria with PEPCK as an importantβ-carboxylation enzyme. Newly available genomic information has confirmed the existence of putativePEPCKgenes in a number of cyanobacterial species. This project represents the first structural and physicochemical study of cyanobacterial PEPCKs. Biocomputational analyses of cyanobacterial PEPCKs were performed and a homology model ofCyanothecesp. PCC 7424 PEPCK was generated. The modeled enzyme consists of an N-terminal and C-terminal domains with a mixedα/βtopology with the active site located in a deep cleft between the two domains. Active site residues and those involved in metal ion coordination were found to be conserved in the cyanobacterial enzymes. An active site lid which is known to close upon substrate binding was also predicted. Amino acid stretches that are unique to cyanobacterial PEPCKs were also identified.

Biocomputational analysis of phosphoenolpyruvate carboxykinase fromRaillietina echinobothrida, a cestode parasite, and its interaction with possible modulators

“…71·91 and 72·09, respectively), indicating that the protein is stable at wide range of temperature as in other PEPCKs (Smith and Caruso, 2013). 71·91 and 72·09, respectively), indicating that the protein is stable at wide range of temperature as in other PEPCKs (Smith and Caruso, 2013).…”

“…2012), S. mansoni (Swargiary et al . 2013), and Cyanobacteria (Smith and Caruso, 2013). In the present study, a homology model was prepared using the crystal structure of rat cytosolic PEPCK as template, and this shows a sequence identity of 54·5% containing all the active sites and catalytic domains of the protein.…”

“…The parasite, R. echinobothrida, was collected from the small intestine of chicken, and morphologically identified by the presence of a heavily armed rostellum with two rows of hooklets and four circular suckers on the scolex (Soulsby, 1982). Immediately, total RNA was isolated from the parasite using Purelink RNA mini kit following manufacturers' protocol.…”

“…formation of phosphoenolpyruvate (PEP) from oxaloacetic acid (OAA), in higher organisms. Cestode parasites mainly depend on carbohydrates for their energy derivation, and have limited ability to metabolize lipids and proteins (Smyth and McManus, 1989). PEPCK uses GTP or ITP (ATP in bacteria and yeast) and metal ions for its activity.…”

Computational Analysis of the Hypothetical Protein P9303_05031 from Marine Cyanobacterium Prochlorococcus Marinus MIT 9303

“…As there is an enormous amount of data present in publicly available databases, making use of such data would help in the characterization of proteins using computational methods. Generally, for computational characterization of any hypothetical protein, the following steps were performed such as prediction of Physico-chemical proteins, prediction of secondary structure, and prediction tertiary structure [ 8 ], [ 9 ]. In this report, we have selected a hypothetical protein of a cyanobacterium Prochlorococcus marinus MIT 9303.…”