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A novel transcriptional regulator of L-arabinose utilization in human gut bacteria.

Chang C, Tesar C, Li X, Kim Y, Rodionov DA, Joachimiak A - Nucleic Acids Res. (2015)

Bottom Line: L-arabinose was confirmed to be a negative effector of BtAraR.In the structure of the BtAraR-DNA complex, we found the unique interaction of arginine intercalating its guanidinum moiety into the base pair stacking of B-DNA.L-arabinose binding induces movement of wHTH domains, resulting in a conformation unsuitable for DNA binding.

View Article: PubMed Central - PubMed

Affiliation: Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.

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Protein–DNA interaction in BtAraR–DNA complex. (A) Overall structure of BtAraR in complex with DNA double strands. BtAraR is represented as ribbon diagram with molecule A colored as green, molecule B as blue. Specific double stranded DNA is represented as stick model with strand C colored as yellow, strand D as purple. (B) The interactions in major groove. The DNA duplex is represented as stick model with carbon color of yellow. The protein molecule is represented with ribbon model while the residues interacting with DNA are stick model. The residues making interactions are all labeled. The hydrogen bonds are indicated as black dotted lines. (C) The interactions in minor groove. The protruding wing in the C-terminal domain is fitted to the minor groove of the DNA duplex. The apo form of BtAraR is represented as dark blue while the protein in complex with DNA is represented as green. The DNA-interacting residues are shown as stick model and the DNA model is represented as stick model with carbon color of yellow. The arrows show the adaptation of Lys204 and Arg205 for fitting on the DNA minor groove. (D) Electron density map around side chain of Arg180. The DNA duplex and protein are represented as stick model. Electron density map (2Fo–Fc) contour level is 1.7 σ.
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Figure 5: Protein–DNA interaction in BtAraR–DNA complex. (A) Overall structure of BtAraR in complex with DNA double strands. BtAraR is represented as ribbon diagram with molecule A colored as green, molecule B as blue. Specific double stranded DNA is represented as stick model with strand C colored as yellow, strand D as purple. (B) The interactions in major groove. The DNA duplex is represented as stick model with carbon color of yellow. The protein molecule is represented with ribbon model while the residues interacting with DNA are stick model. The residues making interactions are all labeled. The hydrogen bonds are indicated as black dotted lines. (C) The interactions in minor groove. The protruding wing in the C-terminal domain is fitted to the minor groove of the DNA duplex. The apo form of BtAraR is represented as dark blue while the protein in complex with DNA is represented as green. The DNA-interacting residues are shown as stick model and the DNA model is represented as stick model with carbon color of yellow. The arrows show the adaptation of Lys204 and Arg205 for fitting on the DNA minor groove. (D) Electron density map around side chain of Arg180. The DNA duplex and protein are represented as stick model. Electron density map (2Fo–Fc) contour level is 1.7 σ.

Mentions: The two apo structures are almost identical with an r.m.s deviation between the two structures of 0.42 Å. Interestingly, the apo–BtAraR proteins are more similar to the structure of AraR in complex with DNA than to the protein in complex with L-arabinose. An r.m.s. deviation between apo-1–BtAraR and the BtAraR–DNA complex is 1.13 Å, while that between apo-1–BtAraR and the L-arabinose-bound complex is 4.54 Å. The largest differences between the apo forms and the BtAraR–DNA complex are observed in the wing of the HTH motif. In the complex with DNA, the AraR β-hairpin loop, which includes two positively charged residues Lys204 and Arg205, moves toward the minor groove of the DNA. This is not observed in the apo structures. The Cα of Lys204 is moved about 4.2 Å and the Cα of Arg205 is moved about 6.1 Å toward the minor groove of the DNA (Figure 5C). In the L-arabinose-bound form, the C-terminal domains of the dimer are closer to each other as compared to the apo forms or the DNA-bound form. The details of these differences are discussed below.


A novel transcriptional regulator of L-arabinose utilization in human gut bacteria.

Chang C, Tesar C, Li X, Kim Y, Rodionov DA, Joachimiak A - Nucleic Acids Res. (2015)

Protein–DNA interaction in BtAraR–DNA complex. (A) Overall structure of BtAraR in complex with DNA double strands. BtAraR is represented as ribbon diagram with molecule A colored as green, molecule B as blue. Specific double stranded DNA is represented as stick model with strand C colored as yellow, strand D as purple. (B) The interactions in major groove. The DNA duplex is represented as stick model with carbon color of yellow. The protein molecule is represented with ribbon model while the residues interacting with DNA are stick model. The residues making interactions are all labeled. The hydrogen bonds are indicated as black dotted lines. (C) The interactions in minor groove. The protruding wing in the C-terminal domain is fitted to the minor groove of the DNA duplex. The apo form of BtAraR is represented as dark blue while the protein in complex with DNA is represented as green. The DNA-interacting residues are shown as stick model and the DNA model is represented as stick model with carbon color of yellow. The arrows show the adaptation of Lys204 and Arg205 for fitting on the DNA minor groove. (D) Electron density map around side chain of Arg180. The DNA duplex and protein are represented as stick model. Electron density map (2Fo–Fc) contour level is 1.7 σ.
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Figure 5: Protein–DNA interaction in BtAraR–DNA complex. (A) Overall structure of BtAraR in complex with DNA double strands. BtAraR is represented as ribbon diagram with molecule A colored as green, molecule B as blue. Specific double stranded DNA is represented as stick model with strand C colored as yellow, strand D as purple. (B) The interactions in major groove. The DNA duplex is represented as stick model with carbon color of yellow. The protein molecule is represented with ribbon model while the residues interacting with DNA are stick model. The residues making interactions are all labeled. The hydrogen bonds are indicated as black dotted lines. (C) The interactions in minor groove. The protruding wing in the C-terminal domain is fitted to the minor groove of the DNA duplex. The apo form of BtAraR is represented as dark blue while the protein in complex with DNA is represented as green. The DNA-interacting residues are shown as stick model and the DNA model is represented as stick model with carbon color of yellow. The arrows show the adaptation of Lys204 and Arg205 for fitting on the DNA minor groove. (D) Electron density map around side chain of Arg180. The DNA duplex and protein are represented as stick model. Electron density map (2Fo–Fc) contour level is 1.7 σ.
Mentions: The two apo structures are almost identical with an r.m.s deviation between the two structures of 0.42 Å. Interestingly, the apo–BtAraR proteins are more similar to the structure of AraR in complex with DNA than to the protein in complex with L-arabinose. An r.m.s. deviation between apo-1–BtAraR and the BtAraR–DNA complex is 1.13 Å, while that between apo-1–BtAraR and the L-arabinose-bound complex is 4.54 Å. The largest differences between the apo forms and the BtAraR–DNA complex are observed in the wing of the HTH motif. In the complex with DNA, the AraR β-hairpin loop, which includes two positively charged residues Lys204 and Arg205, moves toward the minor groove of the DNA. This is not observed in the apo structures. The Cα of Lys204 is moved about 4.2 Å and the Cα of Arg205 is moved about 6.1 Å toward the minor groove of the DNA (Figure 5C). In the L-arabinose-bound form, the C-terminal domains of the dimer are closer to each other as compared to the apo forms or the DNA-bound form. The details of these differences are discussed below.

Bottom Line: L-arabinose was confirmed to be a negative effector of BtAraR.In the structure of the BtAraR-DNA complex, we found the unique interaction of arginine intercalating its guanidinum moiety into the base pair stacking of B-DNA.L-arabinose binding induces movement of wHTH domains, resulting in a conformation unsuitable for DNA binding.

View Article: PubMed Central - PubMed

Affiliation: Midwest Center for Structural Genomics, Argonne National Laboratory, Argonne, IL 60439, USA Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL 60439, USA.

Show MeSH
Related in: MedlinePlus