Difference between revisions of "Binding of R2 to OA operator"
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|<math>K_{d2}</math> | |<math>K_{d2}</math> | ||
− | |<math>0.1 - 5.6 </math> <ref name="Kamionka2004"> </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> | + | |<math>0.1 - 5.6 </math> <ref name="Kamionka2004"> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC373327/pdf/gkh200.pdf 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"> [http://nar.oxfordjournals.org/content/40/18/9340.full-text-lowres.pdf 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"> [http://jb.asm.org/content/189/18/6655.full.pdf 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> |
|<math> nM </math> | |<math> nM </math> | ||
| TetR-tetO interaction and | | TetR-tetO interaction and | ||
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|<math>k^{-}_{2}</math> | |<math>k^{-}_{2}</math> | ||
− | |<math>0.6-1.2</math> <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 | + | |<math>0.6-1.2</math> <ref name="Krok2005"> [http://pubs.acs.org/doi/pdf/10.1021/bi048548w 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> <ref name="Li2012"> [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3416628/pdf/zam6009.pdf 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.] </ref> |
|<math> min^{-1}</math> | |<math> min^{-1}</math> | ||
|SPR of a TetR-like protein (RolR) on a Gram and | |SPR of a TetR-like protein (RolR) on a Gram and |
Revision as of 15:26, 9 October 2015
The ScbR homo-dimer (R2) binds to the ScbA gene operator (OA) and represses its mRNA transcription.
Contents
Chemical equation
Rate equation
Parameters
The parameters of this reaction are the dissociation constant for binding of ScbR to OA () and the dissociation rate for binding of ScbR to OA ().
Name | Value | Units | Origin | Remarks |
---|---|---|---|---|
[1] [2] [3] | 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 OA | ||
[4] [5] | 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 is decided to be and the confidence interval . This means that the mode of the PDF is 5 and the range where 95% of the values are found is between 4.55 and 5.5 nM.
In a similar way, the most plausible value for is and the confidence interval . 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 .
The probability distributions for the two parameters, adjusted accordingly in order to reflect the above values, are the following:
The location and scale parameters of the distributions are:
Parameter | μ | σ |
---|---|---|
References
- ↑ 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.
- ↑ 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.
- ↑ 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.
- ↑ 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
- ↑ 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.