Coding
tphC_322aa

Part:BBa_K808001

Designed by: Valentina Herbring, Sebastian Palluk, Andreas Schmidt   Group: iGEM12_TU_Darmstadt   (2012-08-11)

tphC: terephtalate periplasmatic binding proteine of the tripartite transporter family


Figure 1. Homology modelling of tphC_322 with Phyre2 A-D A. The model of tphC_322 B. Crystal structure of bugT C. Crystal structure of bugD D. Crystal structure of bug27. Images coloured by rainbow N to C terminus.
Figure 1. Results of SignalP 4.0 Server prediction of tphC_322. TphC_322 has a signal peptide and a cleavage site between amino acid 26 and 27

The putative terephtalate periplasmatic binding proteine (tphC_322, 34,38 kDa) was isolated from Comamonas testosteroni KF-1. The strain was purchased from DMSZ-German Collection of Microorganism and Cell Cultures (DMSZ no. 14576). The original sequence contains a PstI recognition site.To eliminate this recognition site a directed-site mutagenic PCR was performed. (For more datails: [http://2012.igem.org/Team:TU_Darmstadt/Protocols/mutagenic_PCR mutagenic PCR]) To characterized the structure of the tphC_322 bioinformatic tools like Protein Homology/anologY Recognition Engine V 2.0 (Phyre2), SignalIP 4.0 Server and TatP 1.0 Server was used. The homology modelling of the tphC_322 with Phyre2 shows 35% identity with BugT (Fig. 1.B,PDB entry 2DVZ) , 31 % identity with transport protein bugD (Fig.1.C,PDB entry [http://www.rcsb.org/pdb/explore.do?structureId=2f5x 2F5X)] and 28 % identity with transport proten bug27 (Fig. 1.D,PDB entry [http://www.rcsb.org/pdb/explore/explore.do?structureId=2QPQ 2QPQ)]. All this proteins play a role in the transport of small molecules into the cell of Bordetella pertussis and belong to the group of periplasmatic bindig proteins of the tripartite tricarboxylate family. The tripartite tricarboxylate transporter system consists of three different proteins: a periplasmatic solute binding receptor (in this case tphC_322), a membrane protein with 12 putative transmembrane alpha-helical spanners, and a small poorly conserved membrane proteine with four putative transmembrane alpha-helical spanners.[1]The structure similarity (Fig.1 A-D) of the tphC_322 with BugT, BugD and Bug27 suggest that the tphC_322 also belongs to the tripartite tricarboxylate transporter family. SignalP 4.0 Server results show, that tphC_322 has a signal peptide and a cleavage site between amino acid 26 and 27.(Fig.3) The TatP 1.0 Server predicted no significant Twin-argenine signal peptide. (Data not shown). It´s suggest that the tphC_322 passes the inner membrane via the Sec protein-translocation pathway.























Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 885
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 211
    Illegal NgoMIV site found at 643
  • 1000
    COMPATIBLE WITH RFC[1000]


References

  • [1] Sasoh, M., E. Masai, et al. (2006). "Characterization of the terephthalate degradation genes of Comamonas sp. strain E6." Appl Environ Microbiol 72(3): 1825-1832.
  • Fukuhara, Y., K. Inakazu, et al. (2010). "Characterization of the isophthalate degradation genes of Comamonas sp. strain E6." Appl Environ Microbiol 76(2): 519-527.
  • Kamimura, N., T. Aoyama, et al. (2010). "Characterization of the protocatechuate 4,5-cleavage pathway operon in Comamonas sp. strain E6 and discovery of a novel pathway gene." Appl Environ Microbiol 76(24): 8093-8101.
  • Winnen, B., R. N. Hvorup, et al. (2003). "The tripartite tricarboxylate transporter (TTT) family." Res Microbiol 154(7): 457-465.
  • Protein structure prediction on the web: a case study using the PhyreKelley LA and Sternberg MJE.Nature Protocols 4, 363 - 371 (2009 server
  • Yang Zhang. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics, vol 9, 40 (2008).
  • Ambrish Roy, Alper Kucukural, Yang Zhang. I-TASSER: a unified platform for automated protein structure and function prediction. Nature Protocols, vol 5, 725-738 (2010).
  • Ambrish Roy, Jianyi Yang, Yang Zhang. COFACTOR: An accurate comparative algorithm for structure-based protein function annotation. Nucleic Acids Research, doi:10.1093/nar/gks372 (2012)
  • Prediction of twin-arginine signal peptides. Jannick Dyrløv Bendtsen, Henrik Nielsen, David Widdick, Tracy Palmer and Søren Brunak. BMC bioinformatics 2005 6: 167.
  • SignalP 4.0: discriminating signal peptides from transmembrane regions Thomas Nordahl Petersen, Søren Brunak, Gunnar von Heijne & Henrik Nielsen Nature Methods, 8:785-786, 2011
  • Erik L.L. Sonnhammer, Gunnar von Heijne, and Anders Krogh:A hidden Markov model for predicting transmembrane helices in protein sequences. In Proc. of Sixth Int. Conf. on Intelligent Systems for Molecular Biology, p 175-182,Ed J. Glasgow, T. Littlejohn, F. Major, R. Lathrop, D. Sankoff, and C. Sensen Menlo Park, CA: AAAI Press, 1998


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