Difference between revisions of "Binding of R2 to OR operator"

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|<math>0.1 - 5.6 </math> <ref name="Kamionka2004"> Kamionka A, Bogdanska-Urbaniak J, Scholz O, Hillen W. ''Two mutations in the tetracycline repressor change the inducer anhydrotetracycline to a corepressor.'' Nucleic Acids Research. 2004;32(2):842-847.</ref> <ref name="Bolla2012"> Bolla JR, Do SV, Long F, et al. ''Structural and functional analysis of the transcriptional regulator Rv3066 of Mycobacterium tuberculosis.'' Nucleic Acids Research. 2012;40(18):9340-9355. </ref> <ref name="Ahn2007"> Ahn SK, Tahlan K, Yu Z, Nodwell J. ''Investigation of Transcription Repression and Small-Molecule Responsiveness by TetR-Like Transcription Factors Using a Heterologous Escherichia coli-Based Assay.'' Journal of Bacteriology. 2007;189(18):6655-6664.</ref> <ref name="Krok2005"> Sylwia Kedracka-Krok, Andrzej Gorecki, Piotr Bonarek, and Zygmunt Wasylewski. ''Kinetic and Thermodynamic Studies of Tet Repressor−Tetracycline Interaction.'' Biochemistry 2005 44 (3), 1037-1046</ref>
 
|<math>0.1 - 5.6 </math> <ref name="Kamionka2004"> Kamionka A, Bogdanska-Urbaniak J, Scholz O, Hillen W. ''Two mutations in the tetracycline repressor change the inducer anhydrotetracycline to a corepressor.'' Nucleic Acids Research. 2004;32(2):842-847.</ref> <ref name="Bolla2012"> Bolla JR, Do SV, Long F, et al. ''Structural and functional analysis of the transcriptional regulator Rv3066 of Mycobacterium tuberculosis.'' Nucleic Acids Research. 2012;40(18):9340-9355. </ref> <ref name="Ahn2007"> Ahn SK, Tahlan K, Yu Z, Nodwell J. ''Investigation of Transcription Repression and Small-Molecule Responsiveness by TetR-Like Transcription Factors Using a Heterologous Escherichia coli-Based Assay.'' Journal of Bacteriology. 2007;189(18):6655-6664.</ref> <ref name="Krok2005"> Sylwia Kedracka-Krok, Andrzej Gorecki, Piotr Bonarek, and Zygmunt Wasylewski. ''Kinetic and Thermodynamic Studies of Tet Repressor−Tetracycline Interaction.'' Biochemistry 2005 44 (3), 1037-1046</ref>
 
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| <math>nM</math>
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| TetR-tetO interaction and  
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| TetR-tetO interaction and TetR-like Rv3066 from ''M. tuberculosis''
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TetR-like Rv3066 from ''M. tuberculosis''
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| rowspan="2" |Repressor protein TetR binds to the operator tetO, repressing its own expression and that of the efflux determinant tetA. Similar structure and activity as ScbR binding to O<sub>R</sub>
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| rowspan="2" |Repressor protein TetR binds to the operator tetO, repressing its own expression and that  
 
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of the efflux determinant tetA. Similar structure and activity as ScbR binding to O<sub>R</sub>
 
 
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|<math>k^{-}_{1}</math>
 
|<math>k^{-}_{1}</math>

Revision as of 00:27, 5 October 2015

The ScbR homo-dimer (R2) binds to its own gene operator (OR) and represses its mRNA transcription.

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Chemical equation

O_{R} + 2R_{2} \rightleftharpoons O_{R}-R_{2}

Rate equation

r= \frac{k^{-}_{1}}{K_{d1}}\cdot [O_{R}]\cdot [R_{2}]^{2} - k^{-}_{1}\cdot [O_{R}-R_{2}]

Parameters

The parameters of this reaction are the dissociation constant for binding of ScbR to OR (K_{d1}) and the dissociation rate for binding of ScbR to OR (k^{-}_{1}).

Name Value Units Origin Remarks
K_{d1} 0.1 - 5.6 [1] [2] [3] [4] nM TetR-tetO interaction and TetR-like Rv3066 from M. tuberculosis Repressor protein TetR binds to the operator tetO, repressing its own expression and that of the efflux determinant tetA. Similar structure and activity as ScbR binding to OR
k^{-}_{1} 0.6-1.2 [4] [5] min^{-1} SPR of a TetR-like protein (RolR) on a Gram and GC content ~ 50-60% from Corynebacterium glutamicum

Parameters with uncertainty

The most plausible parameter value for the K_{d1} is decided to be 4.5 nM and the confidence interval 1.2 . This means that the mode of the PDF is 4.5 and the range where 95% of the values are found is between 3.75 and 5.4 nM.

In a similar way, the most plausible value for k^{-}_{1} is 0.9 min^{-1} and the confidence interval 1.3. This means that the mode of the PDF is 0.9 and the range where 95% of the values are found is between 0.6923 and 1.17 min^{-1}.

The probability distributions for the two parameters, adjusted accordingly in order to reflect the above values, are the following:

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The location and scale parameters of the distributions are:

Parameter μ σ
K_{d1} 1.5126 0.0926
k^{-}_{1} -0.0878 0.1327

References

  1. ↑ Kamionka A, Bogdanska-Urbaniak J, Scholz O, Hillen W. Two mutations in the tetracycline repressor change the inducer anhydrotetracycline to a corepressor. Nucleic Acids Research. 2004;32(2):842-847.
  2. ↑ Bolla JR, Do SV, Long F, et al. Structural and functional analysis of the transcriptional regulator Rv3066 of Mycobacterium tuberculosis. Nucleic Acids Research. 2012;40(18):9340-9355.
  3. ↑ Ahn SK, Tahlan K, Yu Z, Nodwell J. Investigation of Transcription Repression and Small-Molecule Responsiveness by TetR-Like Transcription Factors Using a Heterologous Escherichia coli-Based Assay. Journal of Bacteriology. 2007;189(18):6655-6664.
  4. ↑ 4.0 4.1 Sylwia Kedracka-Krok, Andrzej Gorecki, Piotr Bonarek, and Zygmunt Wasylewski. Kinetic and Thermodynamic Studies of Tet Repressor−Tetracycline Interaction. Biochemistry 2005 44 (3), 1037-1046 Cite error: Invalid <ref> tag; name "Krok2005" defined multiple times with different content
  5. ↑ Li T, Zhao K, Huang Y, et al. The TetR-Type Transcriptional Repressor RolR from Corynebacterium glutamicum Regulates Resorcinol Catabolism by Binding to a Unique Operator, rolO. Applied and Environmental Microbiology. 2012;78(17):6009-6016.
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