Volume 11, Issue 9, Pages 1133-1140 (September 2003) Crystal Structure of Dissimilatory Sulfite Reductase D (DsrD) Protein—Possible Interaction with B- and Z-DNA by Its Winged-Helix Motif  Nobuhiro Mizuno, Gerrit Voordouw, Kunio Miki, Akinori Sarai, Yoshiki Higuchi  Structure  Volume 11, Issue 9, Pages 1133-1140 (September 2003) DOI: 10.1016/S0969-2126(03)00156-4

Figure 1 Stereo View of DsrD Molecules Mol-A and Mol-B in a Dimeric Structure Approximately Perpendicular to the Local 2-Fold Axis Five sulfates on the surface are indicated in the space-filling model. Structure 2003 11, 1133-1140DOI: (10.1016/S0969-2126(03)00156-4)

Figure 2 Comparison of DsrD with Its Homolog (A) Sequence alignment of DsrD from Desulfovibrio vulgaris Hildenborough (DsrD-Dv), the DsrD fragment (residues 405–483) from Bilophila wadsworthia (DsrD-Bw), DsrD from Desulfotomaculum thermocisternum (DsrD-Dt), DsrD from Archaeoglobus fulgidus (DsrD-Af), DsrD from Archaeoglobus profundus (DsrD-Ap), the Zα domain of double-stranded RNA adenosine deaminase (Zα ADAR1), the Zα domain of tumor stroma and activated macrophage protein DLM-1 (Zα DLM), the transcriptional repressor SmtB (SmtB), and the histone H5 globular domain (H5). HNF-3γ is listed because it has a typical B-DNA binding winged-helix motif (HNF-3γ). Box, highly conserved hydrophobic residues in the winged-helix motif; purple, highly conserved residues in the DsrD family; cyan, basic residues; pink, Z-DNA-interacting residues; green, B-DNA-interacting residues (B) Stereo view of four DALI homologs superimposed on the DsrD molecule (Mol-B) and HNF3-γ. Molecules are colored in green (DsrD), blue (Zα ADAR1), red (Zα DLM), cyan (SmtB), purple (H5), and yellow (HNF-3γ). Structure 2003 11, 1133-1140DOI: (10.1016/S0969-2126(03)00156-4)

Figure 3 Potential Surfaces of Winged-Helix Motif Molecules Orientated as indicated in (A); (B) DsrD Mol-B; (C) the Zα Domain of ADAR1; (D) SmtB; (E) HNF-3γ. In DsrD, the low-affinity sulfate binding sites are also indicated. The DsrD structure has a surface potential that is distinct from that of both the Z-DNA and B-DNA binding proteins. Structure 2003 11, 1133-1140DOI: (10.1016/S0969-2126(03)00156-4)

Figure 4 Hypothetical Complexes of the DsrD Mol-B Monomer with B-DNA and Z-DNA Modeled on the Crystal Structures of HNF-3γ and the Zα Domain of ADAR1 (A) DsrD plus B-DNA; (B) DsrD plus Z-DNA. The bound sulfates in low affinity are indicated by a ball and stick model. The proteins of the DsrD family have a well-conserved sequence pattern (YWSSGSTT) on the β hairpin between B2 and B3. The contact surface for DNA consists of the β hairpin and helix H3. The β hairpin of DsrD (black) also contributes to the contact surface for DNA (arrows). The low-affinity sulfate binding sites of DsrD are located close to the positions of the backbone phosphates. Structure 2003 11, 1133-1140DOI: (10.1016/S0969-2126(03)00156-4)

Figure 5 Comparison of the Orientations and Distances of the Recognition Helices H3 in Some B-DNA Binding proteins, Dimeric Structures of DsrD (DsrD in Crystal), Model Structure of DsrD, Whose H1 from One Monomer Is Placed between H1 and H4/S2S3 of Another Monomer (DsrD in Model), Catabolite Gene Activator Protein (CAP), and trp Repressor The relative disposition of the putative recognition helices (black) in the dimeric crystal structure of DsrD must be changed for interaction with the major groove of the double stranded B-DNA. Structure 2003 11, 1133-1140DOI: (10.1016/S0969-2126(03)00156-4)