Difference between revisions of "Part:BBa K808003"

 
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<partinfo>BBa_K808003 short</partinfo>
 
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tctB_162: small subunit B1 of the tripartite tricarboxylate transporter family
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The small subunit B1 of the tripartite tricarboxylate transporter family (tctB_162, 17 kDa) was isolated from ''Comamonas testosteroni KF-1.'' The tripartite tricarboxylate transporter system consists of three different proteins: a periplasmatic solute binding receptor, a membrane protein with 12 putative transmembrane alpha-helical spanners (in this case tctB_162), and a small poorly conserved membrane proteine with four putative transmembrane alpha-helical spanners<sup>[1]</sup>.The strain was purchased from Leibniz Institute DMSZ-German Collection of Microorganism and Cell Cultures (DMSZ no. 14576). The original sequence contains a Pst1 recognition site. To eliminate this recognition site a directed-site mutagenic PCR was performed. (For more datails: link zu dem PCR protokoll und dem Labjournal, wo isolations PCR  beschrieben wird) To characterized the structure of the tctB_162 bioinformatic tools like  '''P '''rotein  '''H '''omology/anolog '''Y '''  '''R '''ecognition  '''E '''ngine V 2.0 (PHYRE2), I-TASSER  servers, protein  '''B '''asic  '''L '''ocal  '''A '''ligment  '''S '''earch  '''T '''ool (BLAST)  and TMHMM was used. The TMHMM predicted a  transmembrane protein with 5 alpha-helical spanners (Fig. 1). The N-teminus is with a probability of over 99 % in cytoplasmatic. The NCBI Protein BLAST results shows that the tctB_162 subunit B1 belongs to the tctB superfamily.
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[[Image:File-tctb162_tmhmm.png|900px|thumb|center|Figure 1. '''TMHMM prediction of the tctB_162 subunit B1''' It shows 5 alpha-helical spanners.]]
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<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>
 
<partinfo>BBa_K808003 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K808003 SequenceAndFeatures</partinfo>
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==References==
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[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.
  
  

Revision as of 17:17, 23 September 2012

tctB_162: small subunit B1 of the tripartite tricarboxylate transporter family

The small subunit B1 of the tripartite tricarboxylate transporter family (tctB_162, 17 kDa) was isolated from Comamonas testosteroni KF-1. The tripartite tricarboxylate transporter system consists of three different proteins: a periplasmatic solute binding receptor, a membrane protein with 12 putative transmembrane alpha-helical spanners (in this case tctB_162), and a small poorly conserved membrane proteine with four putative transmembrane alpha-helical spanners[1].The strain was purchased from Leibniz Institute DMSZ-German Collection of Microorganism and Cell Cultures (DMSZ no. 14576). The original sequence contains a Pst1 recognition site. To eliminate this recognition site a directed-site mutagenic PCR was performed. (For more datails: link zu dem PCR protokoll und dem Labjournal, wo isolations PCR beschrieben wird) To characterized the structure of the tctB_162 bioinformatic tools like P rotein H omology/anolog Y R ecognition E ngine V 2.0 (PHYRE2), I-TASSER servers, protein B asic L ocal A ligment S earch T ool (BLAST) and TMHMM was used. The TMHMM predicted a transmembrane protein with 5 alpha-helical spanners (Fig. 1). The N-teminus is with a probability of over 99 % in cytoplasmatic. The NCBI Protein BLAST results shows that the tctB_162 subunit B1 belongs to the tctB superfamily.

Figure 1. TMHMM prediction of the tctB_162 subunit B1 It shows 5 alpha-helical spanners.


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal NgoMIV site found at 291
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 55


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.