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

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(Created page with "The ScbR homo-dimer (R<sub>2</sub>) binds to the ScbA gene promoter (O<sub>A</sub>) and represses its mRNA transcription. ==Chemical equation== <center><math>O_{A} + 2R_{2} ...")
 
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|<math>0.1 - 5.6 nM </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>  
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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>
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|<math> nM </math>
 
| TetR-tetO interaction and  
 
| TetR-tetO interaction and  
 
TetR-like Rv3066 from ''M. tuberculosis''
 
TetR-like Rv3066 from ''M. tuberculosis''
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|<math>k^{-}_{2}</math>
 
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|<math>0.6-1.2 min^{-1}</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.</ref> <ref name="Li2012"> 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>0.6-1.2 min^{-1}</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.</ref> <ref name="Li2012"> 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>
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|<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  
 
GC content ~ 50-60% from ''Corynebacterium glutamicum''
 
GC content ~ 50-60% from ''Corynebacterium glutamicum''

Revision as of 03:30, 24 September 2015

The ScbR homo-dimer (R2) binds to the ScbA gene promoter (OA) and represses its mRNA transcription.

Chemical equation

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

Rate equation

r= \frac{k^{-}_{2}}{K_{d2}}\cdot [O_{A}]\cdot [R_{2}]^{2} - k^{-}_{2}\cdot [O_{A}-R_{2}]

Parameters

The parameters of this reaction are the dissociation constant for binding of ScbR to OA (K_{d2}) and the dissociation rate for binding of ScbR to OA (k^{-}_{2}).

Name Value Units Origin Remarks
K_{d2} 0.1 - 5.6 [1] [2] [3] 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 OA

k^{-}_{2} 0.6-1.2 min^{-1} [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 values and the confidence interval were decided to be:

K_{d2} = 5 \pm 0.6 nM

k^{-}_{2}= 0.9 \pm 0.3 min^{-1}

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

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. ↑ 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.
  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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