American Journal of Biochemistry and Molecular Biology2150-42102150-4253Academic Journals Inc.10.3923/ajbmb.2011.319.336In silico Characterization and Homology Modeling of Cyanobacterial Phosphoenolpyruvate Carboxylase Enzymes with Computational Tools and Bioinformatics Servers]]>SmithAubrey A. PlazasManuela C. 4201114Phosphoenolpyruvate carboxylase (PEPC; EC4.1.1.31) catalyzes the irreversible β-carboxylation of Phosphoenolpyruvate (PEP) to yield Oxaloacetate (OAA) and inorganic Phosphate (Pi). PEPC contributes to photosynthetic and anaplerotic CO2 fixation in higher plants and bacteria. The aim of this study was to determine the physicochemical properties of cyanobacterial PEPCs and to develop 3-dimensional models of selected enzymes. The biocomputational analyses were performed in silico using web-based software and servers. The alignment of cyanobacterial enzymes and secondary structure analysis revealed that there are conserved amino acid substitutions and polymorphisms between PEPCs from marine and fresh water organisms. Furthermore, some marine subgroups seem to possess unique amino acid stretches that may modulate various aspects of catalysis and regulation. Phosphoenolpyruvate carboxylase from Synechococcus PCC 7002, a marine organism, most closely resembles PEPC from fresh water organisms; for this reason, the enzyme was chosen for homology modeling alongside PEPCs from the fresh water strain Anabaena variabilis and the marine cyanobacterium Synechococcus RS 9917. Amino acids and domains that can distinguish between the fresh water and marine PEPCs were identified. Secondary structure analysis and homology modeling suggested that cyanobacterial PEPCs are primarily alpha helical with additional β-sheets flanking the characteristic central β-barrel. The physicochemical characteristics and the 3D models provide a framework for the purification and characterization of cyanobacterial PEPCs.]]>Arnold, K., L. Bordoli, J. Kopp and T. Schwede,200622195201Biou, V., J.F. Gibrat, J.M. Levin, B. Robson and J. Garnier,19882185191Caldwell, P.E., M.R. MacLean and P.R. Norris,2007Sulfobacillus species.]]>15322312240Chen, L.M., T. Omiya, S. Hata and K. Izui,2002Synechococcus vulcanus with unusual allosteric properties.]]>43159169Chen, L.M., K.Z. Li, T. Miwa and K. Izui,2004Arabidopsis changes amino acid metabolism.]]>219440449Combet, C., C. Blanchet, C. Geourjon and G. Deleage,200025147150Deleage G. and B. Roux,19871289294Eisenhaber, F., F. Imperiale, P. Argos and C. Froemmel,199625157168Frishman, D. and P. Argos,19969133142Garnier, J., D.J. Osguthorpe and B. Robson,197812097120Geourjon, C. and G. Deleage,19947157164Guermeur, Y., C. Geourjon, P. Gallinari and G. Deleage,199915413421Gilbert, D.,20032003Guex, N. and M.C. Peitsch,19971827142723Hammami, S.S., R. Chaffai and E. El Ferjani,2004714191426Izui, K., H. Matsumura, T. Furumoto and Y. Kai,2004556984Kai, Y., H. Matsumura, T. Inoue, K. Terada and Y. Nagara et al.,199996823828Karthikeyan, C.V. and G. Gopalaswamy,20093110Ahmed, O.K.,200912246251King, R.D. and M.J.E. Sternberg,1996522982310Knowles, V.L. and W.C. Plaxton,2003Synechocystis sp. PCC 6803.]]>44758763Larkin, M.A., G. Blackshields, N.P. Brown, R. Chenna and P.A. McGettigan et al.,20072329472948Leegood, R.C.,20024 photosynthesis: Principles of CO2 concentration and Prospects for its introduction into C3 plants.]]>53581590Lovell, S.C., I.W. Davis, W.B. Arendall III, P.I.W. de Bakker and J.M. Word et al.,200350437450Matsumura, H., Y. Xie, S. Shirakata, T. Inoue and T. Yoshinaga et al.,20024 form maize and quaternary complex of E. coli phosphoenolpyruvate carboxylases.]]>1017211730O'Leary, B., S.K. Rao, J. Kim and W.C. Plaxton,20092842479724805Rice, P., I. Longden and A. Bleasby,200016276277Rost, B. and C. Sander,19939075587562Rost, B., G. Yachdav and J. Liu,200432W321W326Sikolia, S., J.C. Onyango, E. Beck and J.I. Kinyamario,20093 and C4Photosynthetic species of the centrospermeae along an altitudinal gradient in Western Kenya.]]>54757Smith, A.A., M.W. Coomes and T.E. Smith,2008Synechococcus PCC 7002.]]>812611270Soltani, N., G. Zarrini, Y. Ghasemi, S. Shokravi and L. Baftehchi,2007Fischerella sp. FS 18 under NaCl stress.]]>7931936Stultz, C.M., J.V. White and T.F. Smith,19932305314Tomitani, A., A.H. Knoll, C.M. Cavanaug and T. Ohno,200610354425447Tripp, J.H., S.R. Bench, K.A. Turk, R.A. Foster and B.A. Desany et al.,20104649094Vriend, G.,199085256White, J.V., C.M. Stultz and T.F. Smith,19941193575Kwon, Y.D., S.Y. Lee and P. Kim,2008Escherichia coli overexpressing phosphoenolpyruvate carboxykinase.]]>7211381141