Hindawi Publishing Corporation Structural Biology Volume 2013, Article ID 370820, 10 pages http://dx.doi.org/10.1155/2013/370820 Research Article In Silico Characterization and Homology Modeling of a Cyanobacterial Phosphoenolpyruvate Carboxykinase Enzyme Aubrey A. Smith and Amanda Caruso Department of Biology, Montgomery College-Rockville Campus, 51 Mannakee Street, Rockville, MD 20850, USA Correspondence should be addressed to Aubrey A. Smith; aubrey.smith@montgomerycollege.edu Received 19 October 2012; Revised 18 January 2013; Accepted 4 February 2013 Academic Editor: Manuela Helmer-Citterich Copyright © 2013 A. A. Smith and A. Caruso. his is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. 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 ixation in aquatic ecosystems consisting of photosynthetic cyanobacteria. RuBisCO-based CO 2 ixation is prevalent in cyanobacteria through C 3 intermediates; however, a signiicant amount of carbon lows into C 4 acids during cyanobacterial photosynthesis. his indicates that a C 4 mechanism for inorganic carbon ixation is prevalent in cyanobacteria with PEPCK as an important -carboxylation enzyme. Newly available genomic information has conirmed the existence of putative PEPCK genes in a number of cyanobacterial species. his project represents the irst 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. he modeled enzyme consists of an N-terminal and C-terminal domains with a mixed / topology with the active site located in a deep clet 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 identiied. 1. Introduction Phosphoenolpyruvate carboxykinase (PEPCK; EC 4.1.32) catalyzes the reversible ATP- or GTP-dependent decarboxy- lation of oxaloacetate (OAA) to yield phosphoenolpyruvate (PEP). his reaction uses the phosphate group from the nucleotide triphosphate and, as a result, produces CO 2 and the corresponding nucleoside diphosphate. PEPCK has a strict requirement for divalent cations with Mn 2+ as its best activator [1]. Two classes of PEPCKs exist in nature, and they are classiied 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 signiicant 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]. he crystal structures of PEPCKs from representative species of plants, bacteria, and mammals have been published, and con- servation in metal and substrate binding were conirmed [4]. In mammals, two forms of PEPCKs exist: PEPCK-M, which is expressed in mitochondria, and PEPCK-C, the cytosolic form of the enzyme. Mammalian PEPCK plays a major role in gluconeogenesis and glyceroneogenesis. he enzyme is also a contributor to other downstream processes [7]. he signiicance of the PEPCK reaction has been studied in Streptococcus bovis, Selenomonas ruminantium, and other bacteria where PEPCK was found to be involved in growth initiation and amino acid synthesis [8]. E. coli overexpressing PEPCK exhibited slower growth rate and increased ATP production [9]. PEPCK has also been investigated as the sole anaplerotic enzyme in the yeast Saccharomyces cerevisiae [10]. In plants, where PEPCK isoforms are expressed in various tissues, regulation of the enzyme by phosphorylation is dependent upon location and illumination [11]. he same is true for CAM plants such as Ananas comosus [12].