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. 2021 May 26;22(11):5662. doi: 10.3390/ijms22115662

Figure 4.

Figure 4

Structural characteristics of selected classes of wheat (Triticum aestivum L.) and Arabidopsis thaliana (L. Heynh) TFs involved in drought and other abiotic stresses. Coding and complementary DNA strands are shown in cpk yellow and cpk green sticks, respectively. Residues that interact with DNA are shown in cpk purple sticks and separations are illustrated in black dashed lines. DNA nucleotides (cis-elements) recognized by TFs are in bold. (A) bZIP: Molecular model of the wheat TabZIP2 homodimer (chains A and B) with the 5′-GGCCCACGTGGCCC-3′ ABRE cis-element. The transcription factor consists of basic (light grey) and leucine zipper (purple) regions (modified from [85]). (B) WRKY: Crystal structure of the C-terminal AtWRKY1 domain (PDB accession 1ODH) (traced in purple) illustrating antiparallel β-sheet contacting the 5′-CGATGCGGGTGCA-3′/5-TGCACCCGCATCG-3′) DNA fragment. Two zinc ions are shown in blue. Selected residues contacting DNA are shown at separations of ≤3.5 Å. (C) HD-Zip: Molecular model of the homeodomain (HD) of TaGL9 (purple) in complex with the 5′-GCATTAAATGC-3’/3’-GCATTTAATGC-5’ DNA fragment. The central recognition α-helix (perpendicular to the viewer; marked by an arrow) contains the residues contacting DNA at separations of ≤3.5 Å (modified from [137]). (D) HD-Zip: Molecular features of homo-dimeric TaHDZipI-3 homeodomains (HDs) (traced in purple) in complex with the 5′-CAATCATTGC/5′-GCAATGATTG-3′ cis-element. Mostly central recognition α-helices (perpendicular to the viewer; marked by arrows) carry residues that contact DNA through water (red spheres) mediated interactions at ≤3.4 Å separations (modified from [157]). (E) MYB: Molecular features of wheat TaMYB74 (traced in purple) in complex with the 5′-AGGTGGTTATGC-3′ MYBR1 cis-element. Predicted residues interacting with DNA at ≤3.6 Å separations are shown (modified from [26]). (F) DREB: Molecular model of the AP2 domain of TaDREB3 (traced in purple) in complex with the 5′-ACCGAC-3′/5′-GTCGGT-3′ DRE cis-element. Anti-parallel strands contact DNA at ≤3.4 separations (modified from [158]). (G) SHN: Molecular features of the wheat AP2 domain of TaSHN1 (traced in purple) in complex with the 5′-GCCGAT-3′/5′-GTCGGC-3′ CRT cis-element. Interactions between residues and DNA at ≤3.5 Å separations are shown (modified from [159]). (H) WXPL: Molecular features of wheat TaWXPL1D (traced in purple) in complex with the 5′-GCCGAT-3′/5′-GTCGGC-3′ CRT cis-element. Antiparallel strands carry residues that contact DNA at ≤3.5 Å separations (modified from [27]). Structural images were drawn in the PyMOL Molecular Graphics System v2.3.3 (Schrődinger LLC, Portland, OR, USA) using TF coordinates of 3D models computed and published in our works [26,27,85,137,157,158,159]. The coordinates of the AtWRKY1 domain were taken from the Protein Data Bank (https://www.rcsb.org/pdb, accessed on 14 April 2021).