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Structural and functional basis of transcriptional regulation by TetR family protein CprB from S. coelicolor A3(2).

Bhukya H, Bhujbalrao R, Bitra A, Anand R - Nucleic Acids Res. (2014)

Bottom Line: Binding of the DNA results in the restructuring of the dimeric interface of CprB, inducing a pendulum-like motion of the helix-turn-helix motif that inserts into the major groove.Experiments performed on a subset of DNA sequences from Streptomyces coelicolor A3(2) suggest that CprB is most likely a pleiotropic regulator.Apart from serving as an autoregulator, it is potentially a part of a network of proteins that modulates the γ-butyrolactone synthesis and antibiotic regulation pathways in S. coelicolor A3(2).

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India IITB-Monash Research Academy, Mumbai 400076, Maharashtra, India.

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Detailed intermolecular interactions between CprB and CS. (A) The interactions of HTH with the bases in the major groove and phosphate backbone of CS are shown. The hydrogen bonding interactions are pointed as dashed lines. The DNA bases indicated using prime (A', T', G' and C') correspond to chain F of CS in CprB–CS complex (PDB entry: 4PXI) and the others are from the complementary strand (chain E). (B) Schematic representation of protein interaction with CS. Residues colored in purple, brown, red and cyan are from subunits A, B, C and D, respectively of the CprB–CS complex. The blue and orange colored arrows indicate the base and backbone interacting residues of CprB respectively with CS.
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Figure 2: Detailed intermolecular interactions between CprB and CS. (A) The interactions of HTH with the bases in the major groove and phosphate backbone of CS are shown. The hydrogen bonding interactions are pointed as dashed lines. The DNA bases indicated using prime (A', T', G' and C') correspond to chain F of CS in CprB–CS complex (PDB entry: 4PXI) and the others are from the complementary strand (chain E). (B) Schematic representation of protein interaction with CS. Residues colored in purple, brown, red and cyan are from subunits A, B, C and D, respectively of the CprB–CS complex. The blue and orange colored arrows indicate the base and backbone interacting residues of CprB respectively with CS.

Mentions: To facilitate the interaction of the HTH motif with the CS, the spacer helix α2 orients such that it results in widening of the groove to ∼13 Å (ideal B-form has 11.7 Å). This allows the helix α3 to insert and make protein DNA contacts to achieve specificity of binding via an induced fit mechanism. This effect of the deformation of the DNA is transmitted along the length of the chain causing the adjacent major groove, not interacting with the protein, to be shrunk by ∼10 Å (Supplementary Table S4). The average of all the roll and twist angles in the DNA are around 0.9° and 35.5°, respectively, yielding a global bend of ∼3.5° in the DNA as compared to the standard B-form. The CprB–CS complex is stabilized by a total of around 35 phosphate backbone and 20 direct base contacts, shown in Figure 2A and B. The direct base contacts in the monomers are mostly through the residues K43, G44, Y47 and F48, whereas residues H49, Y47, T42, S33, T31 and K53 interact via the phosphate backbone. Residues Y47, K43, G44 and F48 from α3 of the HTH motif are tightly docked into the major groove of the CS DNA and are the four major amino acids that partake in base contacts. The hydroxyl moiety of residue Y47 forms a hydrogen bond with the phosphate backbone of all the monomers and the T-shape stacking of the phenyl ring occurs with the bases from the DNA major groove. In several instances, due to the heterogeneity of the DNA sequence, these residues in each of the four monomers encounter different bases, creating a diverse environment. For example, K43 in monomer B, C and D forms hydrogen bond contacts with the bases dG’9, dG’12, dC11, dC14 and dT18; however, K43 in monomer A is disordered. Overall, in this scenario, both the hydrophobic region and the positively charged side chain of the K43 interact with various bases of the DNA via non-covalent interactions. Similarly, in the case of F48 in all the four monomers, a difference in the binding was observed. The F48 in monomers A and C stacks with guanine bases, dA3 and dC6, respectively. Whereas the F48 in monomers B and D stacks with dA’4, and dA’1, respectively (Figure 2A and B).


Structural and functional basis of transcriptional regulation by TetR family protein CprB from S. coelicolor A3(2).

Bhukya H, Bhujbalrao R, Bitra A, Anand R - Nucleic Acids Res. (2014)

Detailed intermolecular interactions between CprB and CS. (A) The interactions of HTH with the bases in the major groove and phosphate backbone of CS are shown. The hydrogen bonding interactions are pointed as dashed lines. The DNA bases indicated using prime (A', T', G' and C') correspond to chain F of CS in CprB–CS complex (PDB entry: 4PXI) and the others are from the complementary strand (chain E). (B) Schematic representation of protein interaction with CS. Residues colored in purple, brown, red and cyan are from subunits A, B, C and D, respectively of the CprB–CS complex. The blue and orange colored arrows indicate the base and backbone interacting residues of CprB respectively with CS.
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Figure 2: Detailed intermolecular interactions between CprB and CS. (A) The interactions of HTH with the bases in the major groove and phosphate backbone of CS are shown. The hydrogen bonding interactions are pointed as dashed lines. The DNA bases indicated using prime (A', T', G' and C') correspond to chain F of CS in CprB–CS complex (PDB entry: 4PXI) and the others are from the complementary strand (chain E). (B) Schematic representation of protein interaction with CS. Residues colored in purple, brown, red and cyan are from subunits A, B, C and D, respectively of the CprB–CS complex. The blue and orange colored arrows indicate the base and backbone interacting residues of CprB respectively with CS.
Mentions: To facilitate the interaction of the HTH motif with the CS, the spacer helix α2 orients such that it results in widening of the groove to ∼13 Å (ideal B-form has 11.7 Å). This allows the helix α3 to insert and make protein DNA contacts to achieve specificity of binding via an induced fit mechanism. This effect of the deformation of the DNA is transmitted along the length of the chain causing the adjacent major groove, not interacting with the protein, to be shrunk by ∼10 Å (Supplementary Table S4). The average of all the roll and twist angles in the DNA are around 0.9° and 35.5°, respectively, yielding a global bend of ∼3.5° in the DNA as compared to the standard B-form. The CprB–CS complex is stabilized by a total of around 35 phosphate backbone and 20 direct base contacts, shown in Figure 2A and B. The direct base contacts in the monomers are mostly through the residues K43, G44, Y47 and F48, whereas residues H49, Y47, T42, S33, T31 and K53 interact via the phosphate backbone. Residues Y47, K43, G44 and F48 from α3 of the HTH motif are tightly docked into the major groove of the CS DNA and are the four major amino acids that partake in base contacts. The hydroxyl moiety of residue Y47 forms a hydrogen bond with the phosphate backbone of all the monomers and the T-shape stacking of the phenyl ring occurs with the bases from the DNA major groove. In several instances, due to the heterogeneity of the DNA sequence, these residues in each of the four monomers encounter different bases, creating a diverse environment. For example, K43 in monomer B, C and D forms hydrogen bond contacts with the bases dG’9, dG’12, dC11, dC14 and dT18; however, K43 in monomer A is disordered. Overall, in this scenario, both the hydrophobic region and the positively charged side chain of the K43 interact with various bases of the DNA via non-covalent interactions. Similarly, in the case of F48 in all the four monomers, a difference in the binding was observed. The F48 in monomers A and C stacks with guanine bases, dA3 and dC6, respectively. Whereas the F48 in monomers B and D stacks with dA’4, and dA’1, respectively (Figure 2A and B).

Bottom Line: Binding of the DNA results in the restructuring of the dimeric interface of CprB, inducing a pendulum-like motion of the helix-turn-helix motif that inserts into the major groove.Experiments performed on a subset of DNA sequences from Streptomyces coelicolor A3(2) suggest that CprB is most likely a pleiotropic regulator.Apart from serving as an autoregulator, it is potentially a part of a network of proteins that modulates the γ-butyrolactone synthesis and antibiotic regulation pathways in S. coelicolor A3(2).

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India IITB-Monash Research Academy, Mumbai 400076, Maharashtra, India.

Show MeSH
Related in: MedlinePlus