Original Article
Homology modeling of thermostable YdaP enzyme from Bacillus licheniformis
Year: 2020 | Month: June | Volume 8 | Issue 1
Arnold, F.H. 1998. Design by directed evolution. Acc. Cashem. Res., 31, 125-131
View at Google ScholarBajorath, J., Stenkamp, R. and Aruffo, A. 1994. Knowledge-based model building of proteins: Concepts and examples. Protein Sci., 2, 1798-1810.
View at Google ScholarBlundell, T.L., Sibanda, B.L., Sternberg, M.J.E. and Thornton, J.M. 1987. Knowledge-based prediction of protein structure and the design of novel molecules. Nature, 326, 347-352.
View at Google ScholarBowie, J.U., Lüthy, R. and Eisenberg, D. 1991. A method to identify protein sequences that fold into a known three-dimensional structure. Science, 253, 164-170.
View at Google ScholarChang, Y.Y. and Cronan, J.E., Jr. 1995. Detection by site-specific disulfide cross-linking of a conformational change in binding of Escherschia coli pyruvate oxidase to lipid bilayers. J. Bio. Chem. 270, 7896-7901
View at Google ScholarGoffin, P., Muscariello, L., Lorquet, F., Stukkens, A., Prozzi, D., Sacco, M., Kleerebezem, M. and Hols, P. 2006. Involvement of pyruvate oxidase activity and acetate production in the survival of Lactobacillus plantarum during the stationary phase of aerobic growth. Appl. Environ. Microbiol., 72, 7933-7940
View at Google ScholarJohnson, M.S. and Overigton, J.P. 1993. A structural basis for sequence comparisons: An evaluation of scoring methodologies. J. Mol. Biol., 233, 716-738.
View at Google ScholarJohnson, M.S., Srinivasan, N., Sowdhamini, R. and Blundell, T.L. 1994. Knowledge-based protein modelling. Crit. Rev. Biochem. Mol. Biol., 29, 1-68.
View at Google ScholarJones, D.T. 1999. GenTHREADER: An efficient and reliable protein folds recognition method for genomic sequences. J. Mol. Biol., 287, 797-815
View at Google ScholarJuan, E.C.M., Hoque, M.M., Hossain, M.T., Yamamoto, T., Imamura, S., Suzuki, K., Sekiguchi, T. and Takénaka, A. 2007. The structures of pyruvate oxidase from Aerococcus viridans with cofactors and with a reaction intermediate reveal the flexibility of the active-site tunnel for catalysis. Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun., 63, 900-907.
View at Google ScholarKleywegt, G.J. and Jones, T.A. 1998. Phi/psi-chology: Ramachandran revisited. Structure, 4, 1395-1400.
View at Google ScholarLako, J.D.W., Yengkopiong, J.P., Stafford, W.H.L., Tuffin, M. and Cowan, D.A. 2018. Cloning, expression and characterization of thermostable YdaP from Bacillus licheniformis 9A. Acta Biochim. Pol., 65, 59-66
View at Google ScholarLeichert, L.I.O., Scharf, C. and Hecker, M. 2003. Global characterization of disulfide stress in Bacillus subtilis. J. Bacteriol., 185, 1967-1975.
View at Google ScholarLorquet, F., Goffin, P., Muscariello, L., Baudry, J.B., Ladero, V., Sacco, M., Kleerebezem, M. and Hols, P. 2004. Characterization and functional analysis of the poxB gene, which encodes pyruvate oxidase in Lactobacillus plantarum. J. Bacteriol., 186, 3749-3759.
View at Google ScholarLovell, S.C., Davis, J.W., Arendall, W.B. 3rd., de Bakker, P.I., Word, J.M., Richardson, M.G. and Richardson, J.S. 2001. Structure validation by Calpha geometry phi, psi and Cbeta deviation. Proteins, 50, 437-450.
View at Google ScholarMartin, A.C.R., MacArthur, M.W. and Thorton, J.M. 1997. Assessment of comparative modeling in CASP2. Proteins, 1, 14-28.
View at Google ScholarMather, M., Schopfer, L.M., Massey, V. and Gennis, R.B. 1982. Studies of the flavin adenine dinucleotide binding region in Escherichia coli pyruvate oxidase. J. Biol. Chem., 257, 12887-12892.
View at Google ScholarMuller, Y.A. and Schulz, G.E. 1993. Structure of thiamine and flavindependent enzyme pyruvate oxidase. Science, 259, 965-967.
View at Google ScholarMuller, Y.A., Schumacher, G., Rudolph, R. and Schulz, G.E. 1994. The refined structures of a stabilized mutant and of wild-type pyruvate oxidase from Lactobacillus plantarum. J. Mol. Biol., 237, 315-335.
View at Google ScholarNeumann, P., Weidner, A., Pech, A., Stubbs, M.T. and Tittmann, K. 2008. Structural basis for membrane binding and catalytic activation of the peripheral membrane enzyme pyruvate oxidase from Escherichia coli. Proc. Nat. Acad. Sci., 105, 17390-17395
View at Google ScholarPatton, T.G., Rice, K.C., Foster, M.K. and Bayles, K.W. 2005. The Staphylococcus aureus cidC gene encodes a pyruvate oxidase that affects acetate metabolism and cell death in stationary phase. Mol. Microbiol, 56, 1664-1674
View at Google ScholarRapp, C.S. and Friesner, R.A. 1999. Prediction of loop geometries using a generalized Born model of solvation effect. Proteins, 35, 173-183
View at Google ScholarŠali, A. and Blundell, T.L. 1993. Comparative protein modeling by satisfaction of spatial restraints. J. Mol. Biol., 234, 779-815.
View at Google ScholarŠali, A. and Overington, J.P. 1994. Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protein Sci., 3, 1582-1596.
View at Google ScholarŠali, A., Potterton, L., Yuan, F., Vlijmen, H. and Karplus, M. 1995. Evaluation of comparative protein structure modeling by MODELLER. Proteins, 23, 318-326
View at Google ScholarSánchez, R. and Šali, A. 1997. Advances in comparative proteinstructure modeling. Curr. Opin. Struct. Biol., 7, 206-214.
View at Google ScholarS?nchez, R., Ya, B.A., Feyfant, E. and Šali, A. 1997. Homology protein structure modeling. Trans. Am. Cryst. Assoc., 32, 81-91.
View at Google ScholarSchreiner, M.E. and Eikmanns, B.J. 2005. Pyruvate: Quinone oxidoreductase from Corynebacterium glutamicum: Purification and biochemical characterization. J. Bacteriol., 187, 862-871.
View at Google ScholarSedewitz, B., Schleifer, K.H. and Gotz, F. 1984. Purification and biochemical characterization of pyruvate oxidase from Lactobacillus plantarum. J. Bacteriol., 160, 273-278.
View at Google ScholarShi, J., Blundell, T.L. and Mizuguchi, K. 2001. Sequence structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties. J. Mol. Biol., 310, 243-257
View at Google ScholarSutcliffe, M.J., Hanseef, I., Carney, D. and Blundell, T.L. 1987. Knowledge based modelling of homologue proteins. Part I. Three dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng., 1, 377-384
View at Google ScholarTittmann, K., Wille, G., Golbik, R., Weidner, A., Ghisla, S. and Hübner, G. 2005. Radical phosphate transfer mechanism for the thiamin diphosphate and FAD-dependent pyruvate oxidase from Lactobacillus plantarum. Kinetics coupling of intercofactor electron transfer with phosphate transfer to acetyl-thiamin diphosphate via a transient FAD semiquinone/hydroxyethyl- ThDP radical pair. Biochemistry, 44, 13291-13303.
View at Google ScholarTomar, A., Eiteman, M.A. and Atman, E. 2003. The effect of acetate pathway mutations on the production of pyruvate in Escherichia coli. Appl. Microbiol. Biotechnol., 62, 76-82.
View at Google ScholarWille, G., Meyer, D., Steinmetz, A., Hinze, E., Golbik, R. and Tittmann, K. 2006. The catalytic cycle of a thiamin diphosphate enzyme examined by cryocrystallography. Nat. Chem. Biol., 2, 324-328.
View at Google ScholarZhang, X., Kenneth, W. and Bayles, S.L. 2017. Staphylococcus aureus CidC is a pyruvate: Menaquinone oxidoreductase. Biochemistry, 56, 4819-4829.
View at Google Scholar



