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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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Ribbon diagram of dimeric structure of BtAraR. The N-terminal domain is colored as cyan, the C-terminal domain is colored as green. Molecule B is represented as paled color. The secondary structures are labeled.
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Figure 3: Ribbon diagram of dimeric structure of BtAraR. The N-terminal domain is colored as cyan, the C-terminal domain is colored as green. Molecule B is represented as paled color. The secondary structures are labeled.

Mentions: The overall structure of BtAraR is quite similar to the previously solved NrtR protein (29% sequence identity), an ADP-ribose-dependent transcriptional regulator from S. oneidensis (17). The biological unit appears to be a dimer while a monomer is composed of two domains. The N-terminal domain (residues 1–148, Nudix domain) shows a Nudix hydrolase fold containing three α-helices and a seven-stranded β sheet along with an extra N-terminal helix of less than a turn. The C-terminal domain (residues 149–225) is a winged helix-turn-helix (wHTH) DNA-binding domain that has a protruding β-hairpin as a wing, and it is predicted to bind the major groove surface of the DNA using the HTH motif and the minor groove surface using the wing (Figure 3; Supplementary Figures S1 and S2).


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)

Ribbon diagram of dimeric structure of BtAraR. The N-terminal domain is colored as cyan, the C-terminal domain is colored as green. Molecule B is represented as paled color. The secondary structures are labeled.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4666351&req=5

Figure 3: Ribbon diagram of dimeric structure of BtAraR. The N-terminal domain is colored as cyan, the C-terminal domain is colored as green. Molecule B is represented as paled color. The secondary structures are labeled.
Mentions: The overall structure of BtAraR is quite similar to the previously solved NrtR protein (29% sequence identity), an ADP-ribose-dependent transcriptional regulator from S. oneidensis (17). The biological unit appears to be a dimer while a monomer is composed of two domains. The N-terminal domain (residues 1–148, Nudix domain) shows a Nudix hydrolase fold containing three α-helices and a seven-stranded β sheet along with an extra N-terminal helix of less than a turn. The C-terminal domain (residues 149–225) is a winged helix-turn-helix (wHTH) DNA-binding domain that has a protruding β-hairpin as a wing, and it is predicted to bind the major groove surface of the DNA using the HTH motif and the minor groove surface using the wing (Figure 3; Supplementary Figures S1 and S2).

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