Solution NMR structures reveal unique homodimer formation by a winged helix-turn-helix motif and provide first structures for protein domain family PF10771

Abstract

High-quality NMR structures of the homo-dimeric proteins Bvu3908 (69-residues in monomeric unit) from Bacteroides vulgatus and Bt2368 (74-residues) from Bacteroides thetaiotaomicron reveal the presence of winged helix-turn-helix (wHTH) motifs mediating tight complex formation. Such homo-dimer formation by winged HTH motifs is otherwise found only in two DNA-binding proteins with known structure: the C-terminal wHTH domain of transcriptional activator FadR from E. coli and protein TubR from B. thurigensis, which is involved in plasmid DNA segregation. However, the relative orientation of the wHTH motifs is different and residues involved in DNA-binding are not conserved in Bvu3908 and Bt2368. Hence, the proteins of the present study are not very likely to bind DNA, but are likely to exhibit a function that has thus far not been ascribed to homo-dimers formed by winged HTH motifs. The structures of Bvu3908 and Bt2368 are the first atomic resolution structures for PFAM family PF10771, a family of unknown function (DUF2582) currently containing 128 members.

The C‐terminal domain of the transcriptional regulator BldD from Streptomyces coelicolor A3(2) constitutes a novel fold of winged‐helix domains

“…For example, the CTD of RAP74 (the large subunit of transcription factor IIF) adopts a WHD fold and interacts with the CTD of FCP1 (RNA polymerase II C‐terminal domain phosphatase) through conserved hydrophobic residues exposed from α2 and α3 . Likewise, Bvu3908 from Bacteroides vulgatus and Bt2368 from Bacteroides thetaiotaomicron also utilize their WHD folds to form a homodimer via the interaction of hydrophobic residues from α3 of each subunit . A dual role for PPI and DNA binding has been observed for the WHDs of an E2F‐DP heterodimeric transcription factor .…”

Structural and Functional Characterization of DUF1471 Domains of Salmonella Proteins SrfN, YdgH/SssB, and YahO

“…NMR spectra of SrfN, YahO, and SssB-III were acquired at 20 or 25°C on Varian Inova 600 and 750 instruments as described previously [35] , [36] . Rotational correlation times used to characterize the oligomerization state of SrfN, YahO, and SssB-I were measured using 1 H-detected 1-D 15 N relaxation experiments [26] .…”

“…Sequence-specific resonance assignment of SrfN and YahO was performed in a semi-automated fashion using AutoAssign [39] and CARA [40] . Structures of SrfN and YahO were calculated using automatic NOE assignment in AS-DP [41] and CYANA [42] , followed by iterative manual refinement using CYANA, and final refinement with Xplor-NIH [43] and CNS [44] , [45] as previously described [35] , [36] .…”