Journal of Biological Sciences1727-30481812-5719Asian Network for Scientific Information10.3923/jbs.2016.141.147Shewanella sp. SIB1: Preliminary
Diffraction Data Analysis]]>BudimanCahyo AngkawidjadjaClement KanayaShigenori 42016164Background and Objective: A 22 kDa FK506-binding protein from a psychrophilic bacterium Shewanella sp. SIB1 (SIB1 FKBP22) is a
member of peptidyl prolyl cis-trans isomerase (PPIase). This protein is homodimer with a V-shaped form, consisting of N and C-domains,
that are connected through a long α-helix, responsible for dimerization and PPIase activity, respectively. Understanding on structural
mechanisms behind the function of SIB1 FKBP22 is limited by unsuccessful attempts on crystallization of the full length SIB1 FKBP22
homodimer due to its flexibility and low stability. Despite the isolated N-domain, with the absence of α-helix and C-domain was
successfully crystallized and structurally solved, the comprehensive structural arrangement of SIB1 FKBP22 remains missing. The objective
of this study is to construct a crystallizable SIB1 FKBP22 derivatives consisting of N and C-domains with its α-helix that reflect full length
of SIB1 FKBP22 and a platform for comprehensive structural analysis. Materials and Methods: A monomeric mutant of SIB1 FKBP22 was
constructed by combining two gene fragments encoding Met 8-Ile 205 and Met 1-Ala 60 of the first and second monomer of SIB1 FKBP22,
respectively, with three glycine residues. This design yielded the mutant has tandemly repeated N-domain connected to C-domain
through a long α-helix hence designated as NNC-FKBP22. Results: The NNC-FKBP22 was monomeric in solution implying that it did not
form a V-shaped dimeric structure. The crystallization of NNC-FKBP22 was attempted under sitting-drop vapor diffusion. The crystals were
obtained under 1.0 M sodium citrate with 10 mM CHES/sodium hydroxide at pH 9.5. The crystal was in the space group of P212121 with
unit cell dimension a = 94.635, b = 92.479 and c = 337.327 Å. A complete native data was collected from a rotating anode source to a
resolution of 3.5 Å at 100 K with an Rmerge value of 25.50. Conclusion: The NNC-FKBP22 was successfully crystallized implying that
stabilization of SIB1 FKBP22 under protein engineering platform is promising approach to decipher its atomic structure. Protein
engineering technique used in this study would also be applicable for other cold-adapted proteins with high structural flexibility and low
stability.]]>Goodchild, A., N.F.W. Saunders, H. Ertan, M. Raftery, M. Guilhaus, P.M.G. Curmi and R. Cavicchioli,2004Methanococcoides burtonii.]]>53309321Karl, D.M., D.F. Bird, K. Bjorkman, T. Houlihan, R. Shackelford and L. Tupas,199928621442147Cavicchioli, R., K.S. Siddiqui, D. Andrews and K.R. Sowers,200213253261Thomas, D.N. and G.S. Dieckmann,2002295641644Feller, G. and C. Gerday,20031200208Siddiqui, K.S. and R. Cavicchioli,200675403433Yuan, M., M. Chen, W. Zhang, W. Lu and J. Wang et al.,2012Deinococcus gobiensis: Insights into the extreme environmental adaptations.]]>2012Cavicchioli, R., T. Thomas and P.M.G. Curmi,20004321331Saunders, N.F.W., T. Thomas, P.M.G. Curmi, J.S. Mattick and E. Kuczek et al.,2003Methanogenium frigidum and Methanococcoides burtonii.]]>1315801588Suzuki, Y., M. Haruki, K. Takano, M. Morikawa and S. Kanaya,2004Shewanella sp. SIB1 in cold-adaptation.]]>27113721381Budiman, C., Y. Koga, K. Takano and S. Kanaya,20111252615284Rahfeld, J.U., K.P. Rucknagel, G. Stoller, S.M. Horne, A. Schierhorn, K.D. Young and G. Fischer,1996cis/trans-isomerase of Escherichia coli similarity to Mip-like proteins of pathogenic bacteria.]]>2712213022138Horne, S.M. and K.D. Young,1995Escherichia coli and other species of the Enterobacteriaceae encode a protein similar to the family of Mip-like FK506-binding proteins.]]>163357365Engleberg, N.C., C. Carter, D.R. Weber, N.P. Cianciotto and B.I. Eisenstein,1989Legionella pneumophila gene associated with macrophage infectivity.]]>5712631270Fischer, G., H. Bang and C. Mech,1984cis-trans-isomerization of peptide binding in proline-containing peptides].]]>4311011111, (In German)Lang, K., F.X. Schmid and G. Fischer,1987329268270Lin, L.N., H. Hasumi and J.F. Brandts,1988956256266Davis, J.M., B.A. Boswell and H.P. Bachinger,198926489568962Kiefhaber, T., R. Quaas, U. Hahn and F.X. Schmid,19902930533061Freskgard, P.O., N. Bergenhem, B.H. Jonsson, M. Svensson and U. Carlsson,1992258466468Tan, Y.J., M. Oliveberg, D.E. Otzen and A.R. Fersht,1997269611622Yang, H.P., H.N. Zhong and H.M. Zhou,1997cis-trans isomerase.]]>1338147150Fanghanel, J. and G. Fischer,2004934533478Edlich, F. and G. Fischer,2006Cis/Trans Isomerases.]]>2006pp: 359pp: 359Jakob, R.P. and F.X. Schmid,200837715601575Feige, M.J., S. Groscurth, M. Marcinowski, Y. Shimizu, H. Kessler, L.M. Hendershot and J. Buchner,2009H1 domain controls the assembly and secretion of IgG antibodies.]]>34569579Krishna, M.M., Y. Lin and S.W. Englander,200434310951109Budiman, C., C. Angkawidjaja, H. Motoike, Y. Koga, K. Takano and S. Kanaya,2011Shewanella sp. SIB1: Dimer dissociation by disruption of Val-Leu knot.]]>2017551764Suzuki, Y., O.Y. Win, Y. Koga, K. Takano and S. Kanaya,200557957815784Budiman, C., T. Tadokoro, C. Angkawidjaja, Y. Koga and S. Kanaya,2012Shewanella sp. SIB1.]]>279976986Riboldi-Tunnicliffe, A., B. Konig, S. Jessen, M.S. Weiss and J. Rahfeld et al.,2001Legionella pneumophila.]]>8779783Hu, K., V. Galius and K. Pervushin,2006451198311991Budiman, C., K. Bando, C. Angkawidjaja, Y. Koga, K. Takano and S. Kanaya,2009cis-trans isomerase.]]>27640914101Laemmli, U.K.,1970227680685Goodwin, T.W. and R.A. Morton,194640628632Smyth, M.S. and J.H.J. Martin,200053814Matthews, B.W.,196833491497Li, X.X., X.D. Xu, Y.Y. Dan and M.L. Zhang,20085312611266Derewenda, Z.S.,201066604615