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Neisseria conserved hypothetical protein DMP12 is a DNA mimic that binds to histone-like HU protein.

Wang HC, Wu ML, Ko TP, Wang AH - Nucleic Acids Res. (2013)

Bottom Line: Our gel filtration and analytical ultracentrifugation results showed that the DMP12 monomer interacts with the dimeric form of the bacterial histone-like protein HU.Functionally, HU proteins participate in bacterial nucleoid formation, as well as recombination, gene regulation and DNA replication.The interaction between DMP12 and HU protein might, therefore, play important roles in these DNA-related mechanisms.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.

ABSTRACT
DNA mimic proteins are unique factors that control the DNA-binding activity of target proteins by directly occupying their DNA-binding sites. To date, only a few DNA mimic proteins have been reported and their functions analyzed. Here, we present evidence that the Neisseria conserved hypothetical protein DMP12 should be added to this list. Our gel filtration and analytical ultracentrifugation results showed that the DMP12 monomer interacts with the dimeric form of the bacterial histone-like protein HU. Subsequent structural analysis of DMP12 showed that the shape and electrostatic surface of the DMP12 monomer are similar to those of the straight portion of the bent HU-bound DNA and complementary to those of HU protein dimer. DMP12 also protects HU protein from limited digestion by trypsin and enhances the growth rate Escherichia coli. Functionally, HU proteins participate in bacterial nucleoid formation, as well as recombination, gene regulation and DNA replication. The interaction between DMP12 and HU protein might, therefore, play important roles in these DNA-related mechanisms.

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The crystal structure of DMP12 presents a DNA-like surface. (A) The secondary structural elements are shown above the amino acid sequence, with blue cylinders representing α-helices and green arrows representing β-sheets. (B) A ribbon diagram of two DMP12 monomers in an asymmetric unit. The α-helices and β-sheets were colored red and yellow, respectively, in one DMP12 monomer, and cyan and purple in the other, respectively. Two magnesium ions (orange) were found on the protein surface. (C) Comparison of the surface charge distribution of DMP12 and HU-bound dsDNA. DMP12 electrostatic potential surface is colored by Pymol, with red to blue representing the electrostatic potential from −77 to +77 kBT. The DNA surface is colored according to atomic charge by the same program. The distances between the β-carbons of neighboring acidic residues on DMP12 and the phosphate groups on HU-bound dsDNA were measured, and similar distances between the negative spots on DMP12 and HU-bound dsDNA were found. The pseudo 2-fold symmetries of the Hu-interacting surface of the HU/DNA complex and our proposed HU-DMP12-binding model are indicated by a green rhombus. (D) DMP12’s β-carbons were used to indicate the location of the negatively charged side chains of ASP and GLU on the DMP12 monomer. β-Carbons that were matched in the DNA of the HU-bound dsDNA are labeled as red spheres; non-matched carbons are white. This diagram is shown in stereo. (E) Proposed HU-DMP12–binding model. This model was produced by the alignment of the negatively charged spots and shapes of the DMP12 monomer and the phosphate backbone of HU-bound dsDNA in Figure 2C and D. In this model, the HU-bound dsDNA in the HU/DNA complex (PDB code: 1P78) is overlaid by DMP12.
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gkt201-F2: The crystal structure of DMP12 presents a DNA-like surface. (A) The secondary structural elements are shown above the amino acid sequence, with blue cylinders representing α-helices and green arrows representing β-sheets. (B) A ribbon diagram of two DMP12 monomers in an asymmetric unit. The α-helices and β-sheets were colored red and yellow, respectively, in one DMP12 monomer, and cyan and purple in the other, respectively. Two magnesium ions (orange) were found on the protein surface. (C) Comparison of the surface charge distribution of DMP12 and HU-bound dsDNA. DMP12 electrostatic potential surface is colored by Pymol, with red to blue representing the electrostatic potential from −77 to +77 kBT. The DNA surface is colored according to atomic charge by the same program. The distances between the β-carbons of neighboring acidic residues on DMP12 and the phosphate groups on HU-bound dsDNA were measured, and similar distances between the negative spots on DMP12 and HU-bound dsDNA were found. The pseudo 2-fold symmetries of the Hu-interacting surface of the HU/DNA complex and our proposed HU-DMP12-binding model are indicated by a green rhombus. (D) DMP12’s β-carbons were used to indicate the location of the negatively charged side chains of ASP and GLU on the DMP12 monomer. β-Carbons that were matched in the DNA of the HU-bound dsDNA are labeled as red spheres; non-matched carbons are white. This diagram is shown in stereo. (E) Proposed HU-DMP12–binding model. This model was produced by the alignment of the negatively charged spots and shapes of the DMP12 monomer and the phosphate backbone of HU-bound dsDNA in Figure 2C and D. In this model, the HU-bound dsDNA in the HU/DNA complex (PDB code: 1P78) is overlaid by DMP12.

Mentions: The protein structure of DMP12 provides further evidence of its DNA mimic properties. It contains five α-helices (α1 ∼ α5) and four β-strands in antiparallel configuration (β1 ∼ β4; Figure 2A). The refined crystal structure contains two DMP12 molecules in the asymmetric unit (Figure 2B), with two magnesium ions bound to the surface (Supplementary Figure S4). A structural homology search using the DALI website showed that DMP12 has no similarity to any other known structure, indicating a novel fold.Figure 2.


Neisseria conserved hypothetical protein DMP12 is a DNA mimic that binds to histone-like HU protein.

Wang HC, Wu ML, Ko TP, Wang AH - Nucleic Acids Res. (2013)

The crystal structure of DMP12 presents a DNA-like surface. (A) The secondary structural elements are shown above the amino acid sequence, with blue cylinders representing α-helices and green arrows representing β-sheets. (B) A ribbon diagram of two DMP12 monomers in an asymmetric unit. The α-helices and β-sheets were colored red and yellow, respectively, in one DMP12 monomer, and cyan and purple in the other, respectively. Two magnesium ions (orange) were found on the protein surface. (C) Comparison of the surface charge distribution of DMP12 and HU-bound dsDNA. DMP12 electrostatic potential surface is colored by Pymol, with red to blue representing the electrostatic potential from −77 to +77 kBT. The DNA surface is colored according to atomic charge by the same program. The distances between the β-carbons of neighboring acidic residues on DMP12 and the phosphate groups on HU-bound dsDNA were measured, and similar distances between the negative spots on DMP12 and HU-bound dsDNA were found. The pseudo 2-fold symmetries of the Hu-interacting surface of the HU/DNA complex and our proposed HU-DMP12-binding model are indicated by a green rhombus. (D) DMP12’s β-carbons were used to indicate the location of the negatively charged side chains of ASP and GLU on the DMP12 monomer. β-Carbons that were matched in the DNA of the HU-bound dsDNA are labeled as red spheres; non-matched carbons are white. This diagram is shown in stereo. (E) Proposed HU-DMP12–binding model. This model was produced by the alignment of the negatively charged spots and shapes of the DMP12 monomer and the phosphate backbone of HU-bound dsDNA in Figure 2C and D. In this model, the HU-bound dsDNA in the HU/DNA complex (PDB code: 1P78) is overlaid by DMP12.
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gkt201-F2: The crystal structure of DMP12 presents a DNA-like surface. (A) The secondary structural elements are shown above the amino acid sequence, with blue cylinders representing α-helices and green arrows representing β-sheets. (B) A ribbon diagram of two DMP12 monomers in an asymmetric unit. The α-helices and β-sheets were colored red and yellow, respectively, in one DMP12 monomer, and cyan and purple in the other, respectively. Two magnesium ions (orange) were found on the protein surface. (C) Comparison of the surface charge distribution of DMP12 and HU-bound dsDNA. DMP12 electrostatic potential surface is colored by Pymol, with red to blue representing the electrostatic potential from −77 to +77 kBT. The DNA surface is colored according to atomic charge by the same program. The distances between the β-carbons of neighboring acidic residues on DMP12 and the phosphate groups on HU-bound dsDNA were measured, and similar distances between the negative spots on DMP12 and HU-bound dsDNA were found. The pseudo 2-fold symmetries of the Hu-interacting surface of the HU/DNA complex and our proposed HU-DMP12-binding model are indicated by a green rhombus. (D) DMP12’s β-carbons were used to indicate the location of the negatively charged side chains of ASP and GLU on the DMP12 monomer. β-Carbons that were matched in the DNA of the HU-bound dsDNA are labeled as red spheres; non-matched carbons are white. This diagram is shown in stereo. (E) Proposed HU-DMP12–binding model. This model was produced by the alignment of the negatively charged spots and shapes of the DMP12 monomer and the phosphate backbone of HU-bound dsDNA in Figure 2C and D. In this model, the HU-bound dsDNA in the HU/DNA complex (PDB code: 1P78) is overlaid by DMP12.
Mentions: The protein structure of DMP12 provides further evidence of its DNA mimic properties. It contains five α-helices (α1 ∼ α5) and four β-strands in antiparallel configuration (β1 ∼ β4; Figure 2A). The refined crystal structure contains two DMP12 molecules in the asymmetric unit (Figure 2B), with two magnesium ions bound to the surface (Supplementary Figure S4). A structural homology search using the DALI website showed that DMP12 has no similarity to any other known structure, indicating a novel fold.Figure 2.

Bottom Line: Our gel filtration and analytical ultracentrifugation results showed that the DMP12 monomer interacts with the dimeric form of the bacterial histone-like protein HU.Functionally, HU proteins participate in bacterial nucleoid formation, as well as recombination, gene regulation and DNA replication.The interaction between DMP12 and HU protein might, therefore, play important roles in these DNA-related mechanisms.

View Article: PubMed Central - PubMed

Affiliation: Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.

ABSTRACT
DNA mimic proteins are unique factors that control the DNA-binding activity of target proteins by directly occupying their DNA-binding sites. To date, only a few DNA mimic proteins have been reported and their functions analyzed. Here, we present evidence that the Neisseria conserved hypothetical protein DMP12 should be added to this list. Our gel filtration and analytical ultracentrifugation results showed that the DMP12 monomer interacts with the dimeric form of the bacterial histone-like protein HU. Subsequent structural analysis of DMP12 showed that the shape and electrostatic surface of the DMP12 monomer are similar to those of the straight portion of the bent HU-bound DNA and complementary to those of HU protein dimer. DMP12 also protects HU protein from limited digestion by trypsin and enhances the growth rate Escherichia coli. Functionally, HU proteins participate in bacterial nucleoid formation, as well as recombination, gene regulation and DNA replication. The interaction between DMP12 and HU protein might, therefore, play important roles in these DNA-related mechanisms.

Show MeSH
Related in: MedlinePlus