Allosteric Inhibition of a Zinc-Sensing Transcriptional Repressor: Insights into the Arsenic Repressor (ArsR) Family
The molecular basis of allosteric regulation remains a subject of intense interest. Staphylococcus aureus CzrA is a member of the ubiquitous arsenic repressor (ArsR) family of bacterial homodimeric metal-sensing proteins and has emerged as a model system for understanding allosteric regulation of op...
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| Published in | Journal of molecular biology Vol. 425; no. 7; pp. 1143 - 1157 |
|---|---|
| Main Authors | , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Elsevier Ltd
12.04.2013
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| Subjects | |
| Online Access | Get full text |
| ISSN | 0022-2836 1089-8638 1089-8638 |
| DOI | 10.1016/j.jmb.2013.01.018 |
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| Abstract | The molecular basis of allosteric regulation remains a subject of intense interest. Staphylococcus aureus CzrA is a member of the ubiquitous arsenic repressor (ArsR) family of bacterial homodimeric metal-sensing proteins and has emerged as a model system for understanding allosteric regulation of operator DNA binding by transition metal ions. Using unnatural amino acid substitution and a standard linkage analysis, we show that a His97′ NHε2•••O=C His67 quaternary structural hydrogen bond is an energetically significant contributor to the magnitude of the allosteric coupling free energy, ∆Gc. A “cavity” introduced just beneath this hydrogen bond in V66A/L68V CzrA results in a significant reduction in regulation by Zn(II) despite adopting a wild-type global structure and Zn(II) binding and DNA binding affinities only minimally affected from wild type. The energetics of Zn(II) binding and heterotropic coupling free energies (∆Hc, −T∆Sc) of the double mutant are also radically altered and suggest that increased internal dynamics leads to poorer allosteric negative regulation in V66A/L68V CzrA. A statistical coupling analysis of 3000 ArsR proteins reveals a sector that links the DNA-binding determinants and the α5 Zn(II)-sensing sites through V66/L68 in CzrA. We propose that distinct regulatory sites uniquely characteristic of individual ArsR proteins result from evolution of distinct connectivities to this sector, each capable of driving the same biological outcome, transcriptional derepression.
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► The molecular basis of allosteric regulation or linkage remains a subject of intense interest. ► A zinc-regulated repressor, CzrA, is used to investigate the underpinnings of allostery. ► Selective excision of a quaternary structural hydrogen bond nearly blocks linkage in CzrA. ► Introduction of a “cavity” just below this hydrogen bond also compromises linkage in the absence of a global structural change. ► A statistical coupling analysis reveals a sector that links the DNA binding site and the zinc-sensing site through an allosteric “hot-spot” defined by cavity residues. |
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| AbstractList | The molecular basis of allosteric regulation remains a subject of intense interest. Staphylococcus aureus CzrA is a member of the ubiquitous arsenic repressor (ArsR) family of bacterial homodimeric metal-sensing proteins and has emerged as a model system for understanding allosteric regulation of operator DNA binding by transition metal ions. Using unnatural amino acid substitution and a standard linkage analysis, we show that a His97′ NHε2•••O=C His67 quaternary structural hydrogen bond is an energetically significant contributor to the magnitude of the allosteric coupling free energy, ∆Gc. A “cavity” introduced just beneath this hydrogen bond in V66A/L68V CzrA results in a significant reduction in regulation by Zn(II) despite adopting a wild-type global structure and Zn(II) binding and DNA binding affinities only minimally affected from wild type. The energetics of Zn(II) binding and heterotropic coupling free energies (∆Hc, −T∆Sc) of the double mutant are also radically altered and suggest that increased internal dynamics leads to poorer allosteric negative regulation in V66A/L68V CzrA. A statistical coupling analysis of 3000 ArsR proteins reveals a sector that links the DNA-binding determinants and the α5 Zn(II)-sensing sites through V66/L68 in CzrA. We propose that distinct regulatory sites uniquely characteristic of individual ArsR proteins result from evolution of distinct connectivities to this sector, each capable of driving the same biological outcome, transcriptional derepression.
[Display omitted]
► The molecular basis of allosteric regulation or linkage remains a subject of intense interest. ► A zinc-regulated repressor, CzrA, is used to investigate the underpinnings of allostery. ► Selective excision of a quaternary structural hydrogen bond nearly blocks linkage in CzrA. ► Introduction of a “cavity” just below this hydrogen bond also compromises linkage in the absence of a global structural change. ► A statistical coupling analysis reveals a sector that links the DNA binding site and the zinc-sensing site through an allosteric “hot-spot” defined by cavity residues. The molecular basis of allosteric regulation remains a subject of intense interest. Staphylococcus aureus CzrA is a member of the ubiquitous arsenic repressor (ArsR) family of bacterial homodimeric metal sensing proteins, and has emerged as a model system for understanding allosteric regulation of operator DNA binding by transition metal ions. Using unnatural amino acid substitution and a standard linkage analysis, we show that a His97’ NHε2•••O=C-His67 quaternary structural hydrogen bond is an energetically significant contributor to the magnitude of the allosteric coupling free energy, Δ G c . A “cavity” introduced just beneath this hydrogen bond in V66A/L68V CzrA results in a dramatic loss of regulation by Zn(II) despite adopting a wild-type global structure and Zn(II) binding and DNA binding affinities only minimally affected from wild-type. The energetics of Zn(II) binding and heterotropic coupling free energies (Δ H c , − T Δ S c ) of the double mutant are also radically altered and suggest that increased internal dynamics leads to poorer allosteric negative regulation in V66A/L68V CzrA. A statistical coupling analysis of 3000 ArsR proteins reveals a sector that links the DNA-binding determinants and the α5 Zn(II) sensing sites through V66/L68 in CzrA. We propose that distinct regulatory sites uniquely characteristic of individual ArsR proteins results from evolution of distinct connectivities to this sector, each capable of driving the same biological outcome, transcriptional derepression. The molecular basis of allosteric regulation remains a subject of intense interest. Staphylococcus aureus CzrA is a member of the ubiquitous arsenic repressor (ArsR) family of bacterial homodimeric metal-sensing proteins and has emerged as a model system for understanding allosteric regulation of operator DNA binding by transition metal ions. Using unnatural amino acid substitution and a standard linkage analysis, we show that a His97' NH(ε2)...O=C His67 quaternary structural hydrogen bond is an energetically significant contributor to the magnitude of the allosteric coupling free energy, ∆Gc. A "cavity" introduced just beneath this hydrogen bond in V66A/L68V CzrA results in a significant reduction in regulation by Zn(II) despite adopting a wild-type global structure and Zn(II) binding and DNA binding affinities only minimally affected from wild type. The energetics of Zn(II) binding and heterotropic coupling free energies (∆Hc, -T∆Sc) of the double mutant are also radically altered and suggest that increased internal dynamics leads to poorer allosteric negative regulation in V66A/L68V CzrA. A statistical coupling analysis of 3000 ArsR proteins reveals a sector that links the DNA-binding determinants and the α5 Zn(II)-sensing sites through V66/L68 in CzrA. We propose that distinct regulatory sites uniquely characteristic of individual ArsR proteins result from evolution of distinct connectivities to this sector, each capable of driving the same biological outcome, transcriptional derepression. The molecular basis of allosteric regulation remains a subject of intense interest. Staphylococcus aureus CzrA is a member of the ubiquitous arsenic repressor (ArsR) family of bacterial homodimeric metal-sensing proteins and has emerged as a model system for understanding allosteric regulation of operator DNA binding by transition metal ions. Using unnatural amino acid substitution and a standard linkage analysis, we show that a His97′ NHᵋ²•••O=C His67 quaternary structural hydrogen bond is an energetically significant contributor to the magnitude of the allosteric coupling free energy, ∆Gc. A “cavity” introduced just beneath this hydrogen bond in V66A/L68V CzrA results in a significant reduction in regulation by Zn(II) despite adopting a wild-type global structure and Zn(II) binding and DNA binding affinities only minimally affected from wild type. The energetics of Zn(II) binding and heterotropic coupling free energies (∆Hc, −T∆Sc) of the double mutant are also radically altered and suggest that increased internal dynamics leads to poorer allosteric negative regulation in V66A/L68V CzrA. A statistical coupling analysis of 3000 ArsR proteins reveals a sector that links the DNA-binding determinants and the α5 Zn(II)-sensing sites through V66/L68 in CzrA. We propose that distinct regulatory sites uniquely characteristic of individual ArsR proteins result from evolution of distinct connectivities to this sector, each capable of driving the same biological outcome, transcriptional derepression. The molecular basis of allosteric regulation remains a subject of intense interest. Staphylococcus aureus CzrA is a member of the ubiquitous arsenic repressor (ArsR) family of bacterial homodimeric metal-sensing proteins and has emerged as a model system for understanding allosteric regulation of operator DNA binding by transition metal ions. Using unnatural amino acid substitution and a standard linkage analysis, we show that a His97′ NHε2•••O=C His67 quaternary structural hydrogen bond is an energetically significant contributor to the magnitude of the allosteric coupling free energy, ∆Gc. A “cavity” introduced just beneath this hydrogen bond in V66A/L68V CzrA results in a significant reduction in regulation by Zn(II) despite adopting a wild-type global structure and Zn(II) binding and DNA binding affinities only minimally affected from wild type. The energetics of Zn(II) binding and heterotropic coupling free energies (∆Hc, −T∆Sc) of the double mutant are also radically altered and suggest that increased internal dynamics leads to poorer allosteric negative regulation in V66A/L68V CzrA. A statistical coupling analysis of 3000 ArsR proteins reveals a sector that links the DNA-binding determinants and the α5 Zn(II)-sensing sites through V66/L68 in CzrA. We propose that distinct regulatory sites uniquely characteristic of individual ArsR proteins result from evolution of distinct connectivities to this sector, each capable of driving the same biological outcome, transcriptional derepression. The molecular basis of allosteric regulation remains a subject of intense interest. Staphylococcus aureus CzrA is a member of the ubiquitous arsenic repressor (ArsR) family of bacterial homodimeric metal-sensing proteins and has emerged as a model system for understanding allosteric regulation of operator DNA binding by transition metal ions. Using unnatural amino acid substitution and a standard linkage analysis, we show that a His97' NH(ε2)...O=C His67 quaternary structural hydrogen bond is an energetically significant contributor to the magnitude of the allosteric coupling free energy, ∆Gc. A "cavity" introduced just beneath this hydrogen bond in V66A/L68V CzrA results in a significant reduction in regulation by Zn(II) despite adopting a wild-type global structure and Zn(II) binding and DNA binding affinities only minimally affected from wild type. The energetics of Zn(II) binding and heterotropic coupling free energies (∆Hc, -T∆Sc) of the double mutant are also radically altered and suggest that increased internal dynamics leads to poorer allosteric negative regulation in V66A/L68V CzrA. A statistical coupling analysis of 3000 ArsR proteins reveals a sector that links the DNA-binding determinants and the α5 Zn(II)-sensing sites through V66/L68 in CzrA. We propose that distinct regulatory sites uniquely characteristic of individual ArsR proteins result from evolution of distinct connectivities to this sector, each capable of driving the same biological outcome, transcriptional derepression.The molecular basis of allosteric regulation remains a subject of intense interest. Staphylococcus aureus CzrA is a member of the ubiquitous arsenic repressor (ArsR) family of bacterial homodimeric metal-sensing proteins and has emerged as a model system for understanding allosteric regulation of operator DNA binding by transition metal ions. Using unnatural amino acid substitution and a standard linkage analysis, we show that a His97' NH(ε2)...O=C His67 quaternary structural hydrogen bond is an energetically significant contributor to the magnitude of the allosteric coupling free energy, ∆Gc. A "cavity" introduced just beneath this hydrogen bond in V66A/L68V CzrA results in a significant reduction in regulation by Zn(II) despite adopting a wild-type global structure and Zn(II) binding and DNA binding affinities only minimally affected from wild type. The energetics of Zn(II) binding and heterotropic coupling free energies (∆Hc, -T∆Sc) of the double mutant are also radically altered and suggest that increased internal dynamics leads to poorer allosteric negative regulation in V66A/L68V CzrA. A statistical coupling analysis of 3000 ArsR proteins reveals a sector that links the DNA-binding determinants and the α5 Zn(II)-sensing sites through V66/L68 in CzrA. We propose that distinct regulatory sites uniquely characteristic of individual ArsR proteins result from evolution of distinct connectivities to this sector, each capable of driving the same biological outcome, transcriptional derepression. |
| Author | Dann, Charles E. DiMarchi, Richard D. Giedroc, David P. Ward, Brian P. Ma, Zhen Grossoehme, Nicholas E. Guerra, Alfredo J. Campanello, Gregory C. Ye, Yuzhen |
| AuthorAffiliation | 2 Department of Chemistry, Physics and Geology, Winthrop University, Rock Hill, SC 29733, USA 3 School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405, USA 1 Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA 4 Department of Microbiology, Cornell University, Ithaca, NY 14853 USA |
| AuthorAffiliation_xml | – name: 1 Department of Chemistry, Indiana University, Bloomington, IN 47405-7102, USA – name: 2 Department of Chemistry, Physics and Geology, Winthrop University, Rock Hill, SC 29733, USA – name: 3 School of Informatics and Computing, Indiana University, Bloomington, Indiana 47405, USA – name: 4 Department of Microbiology, Cornell University, Ithaca, NY 14853 USA |
| Author_xml | – sequence: 1 givenname: Gregory C. surname: Campanello fullname: Campanello, Gregory C. organization: Department of Chemistry, Indiana University, Bloomington, IN 47405–7102, USA – sequence: 2 givenname: Zhen surname: Ma fullname: Ma, Zhen organization: Department of Chemistry, Indiana University, Bloomington, IN 47405–7102, USA – sequence: 3 givenname: Nicholas E. surname: Grossoehme fullname: Grossoehme, Nicholas E. organization: Department of Chemistry, Physics and Geology, Winthrop University, Rock Hill, SC 29733, USA – sequence: 4 givenname: Alfredo J. surname: Guerra fullname: Guerra, Alfredo J. organization: Department of Chemistry, Indiana University, Bloomington, IN 47405–7102, USA – sequence: 5 givenname: Brian P. surname: Ward fullname: Ward, Brian P. organization: Department of Chemistry, Indiana University, Bloomington, IN 47405–7102, USA – sequence: 6 givenname: Richard D. surname: DiMarchi fullname: DiMarchi, Richard D. organization: Department of Chemistry, Indiana University, Bloomington, IN 47405–7102, USA – sequence: 7 givenname: Yuzhen surname: Ye fullname: Ye, Yuzhen organization: School of Informatics and Computing, Indiana University, Bloomington, IN 47405, USA – sequence: 8 givenname: Charles E. surname: Dann fullname: Dann, Charles E. organization: Department of Chemistry, Indiana University, Bloomington, IN 47405–7102, USA – sequence: 9 givenname: David P. surname: Giedroc fullname: Giedroc, David P. email: giedroc@indiana.edu organization: Department of Chemistry, Indiana University, Bloomington, IN 47405–7102, USA |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/23353829$$D View this record in MEDLINE/PubMed |
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| Keywords | SCA TROSY statistical coupling analysis zinc sensor ITC metal homeostasis HSQC TCEP allostery ArsR |
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| Snippet | The molecular basis of allosteric regulation remains a subject of intense interest. Staphylococcus aureus CzrA is a member of the ubiquitous arsenic repressor... The molecular basis of allosteric regulation remains a subject of intense interest. Staphylococcus aureus CzrA is a member of the ubiquitous arsenic repressor... |
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| SubjectTerms | Allosteric Regulation allostery Amino Acid Substitution ArsR Bacterial Proteins Bacterial Proteins - chemistry Bacterial Proteins - genetics Bacterial Proteins - metabolism Binding Sites Binding Sites - genetics Binding, Competitive chemistry Crystallography, X-Ray DNA DNA-Binding Proteins DNA-Binding Proteins - chemistry DNA-Binding Proteins - genetics DNA-Binding Proteins - metabolism energy evolution genetics Hydrogen Bonding Kinetics metabolism metal homeostasis metal ions Models, Molecular mutants Mutation Protein Binding Protein Multimerization Protein Structure, Secondary Protein Structure, Tertiary proteins Repressor Proteins Repressor Proteins - chemistry Repressor Proteins - genetics Repressor Proteins - metabolism Staphylococcus aureus Staphylococcus aureus - genetics Staphylococcus aureus - metabolism statistical coupling analysis Thermodynamics transcription (genetics) Transcription, Genetic zinc Zinc - chemistry Zinc - metabolism zinc sensor |
| Title | Allosteric Inhibition of a Zinc-Sensing Transcriptional Repressor: Insights into the Arsenic Repressor (ArsR) Family |
| URI | https://dx.doi.org/10.1016/j.jmb.2013.01.018 https://www.ncbi.nlm.nih.gov/pubmed/23353829 https://www.proquest.com/docview/1317854939 https://www.proquest.com/docview/1672083859 https://pubmed.ncbi.nlm.nih.gov/PMC3602352 |
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