%0 Journal Article
%T In Silico Characterization and Homology Modeling of a Cyanobacterial Phosphoenolpyruvate Carboxykinase Enzyme
%A Aubrey A. Smith
%A Amanda Caruso
%J Structural Biology
%D 2013
%I Hindawi Publishing Corporation
%R 10.1155/2013/370820
%X 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 CO2 fixation is prevalent in cyanobacteria through C3 intermediates; however, a significant amount of carbon flows into C4 acids during cyanobacterial photosynthesis. This indicates that a C4 mechanism for inorganic carbon fixation is prevalent in cyanobacteria with PEPCK as an important ¦Â-carboxylation enzyme. Newly available genomic information has confirmed the existence of putative PEPCK genes 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 of Cyanothece sp. PCC 7424 PEPCK was generated. The modeled enzyme consists of an N-terminal and C-terminal domains with a mixed ¦Á/¦Â topology 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. 1. Introduction Phosphoenolpyruvate carboxykinase (PEPCK; EC 4.1.32) catalyzes the reversible ATP- or GTP-dependent decarboxylation of oxaloacetate (OAA) to yield phosphoenolpyruvate (PEP). This reaction uses the phosphate group from the nucleotide triphosphate and, as a result, produces CO2 and the corresponding nucleoside diphosphate. PEPCK has a strict requirement for divalent cations with Mn2+ as its best activator [1]. Two classes of PEPCKs exist in nature, and they are classified in the basis of the nucleotide substrate: ATP-utilizing enzymes are found in bacteria, plants, and yeast, while GTP-dependent PEPCKs are found mostly in higher eukaryotes [2]. GTP-dependent PEPCKs also occur in some bacteria such as Corynebacterium glutamicum [3]. While there is no significant sequence identity between the two classes, a number of residues are completely conserved across all PEPCKs in the regions of the enzyme that are necessary for nucleotide binding and metal ion coordination [1]. The crystal structures of PEPCKs from representative species of plants, bacteria, and mammals have been published, and conservation in metal and substrate binding were confirmed [4]. In mammals, two forms of
%U http://www.hindawi.com/journals/sb/2013/370820/