Volume 9, Issue 1, Pages 71-85 (January 2016) Structural Aspects of Multistep Phosphorelay-Mediated Signaling in Plants  Blanka Pekárová, Agnieszka Szmitkowska, Radka Dopitová, Oksana Degtjarik, Lukáš Žídek, Jan Hejátko  Molecular Plant  Volume 9, Issue 1, Pages 71-85 (January 2016) DOI: 10.1016/j.molp.2015.11.008 Copyright © 2016 The Author Terms and Conditions

Figure 1 Multistep Phosphorelay in Plants. (A) Model of MSP signaling in Arabidopsis. Signal perception induces autophosphorylation of the histidine residue in the kinase domain of sensor histidine kinases localized in the cytoplasm or in the ER lumen. The phosphoryl group is subsequently transferred intramolecularly to a conserved aspartate residue of the C-terminal receiver domain. AHP proteins accept the signal from histidine kinases. The signal is transferred either to the nucleus, where the signal output is realized via regulation of target gene expression through ARRs-B or via control of effector proteins through ARRs-A. Alternatively, AHPs may remain in the cytoplasm and allow transphosphorylation of ARRs-A, thereby further transferring the signal to target proteins. CRFs (depicted as green horizontal rectangles) are transcription factors, and their function is similar to that of ARRs-B as they work in parallel. One of the ARRs-A target effector proteins is phytochrome B (phyB), here shown as a blue rectangle. ARRs-A also mediate negative feedback regulation by attenuating the signaling. AHP6 and nitric oxide (NO) also negatively regulate cytokinin signaling. Dashed lines show regulation via an unclear molecular mechanism or proposed regulatory interactions. Phosphoryl group is shown as a yellow star. Light is depicted as a yellow sun, and hydrogen peroxide as H2O2. Domain coding is the same as in (B). (B) Schematic representation of the protein domains. Molecular Plant 2016 9, 71-85DOI: (10.1016/j.molp.2015.11.008) Copyright © 2016 The Author Terms and Conditions

Figure 2 CHASE Domain of AHK4. (A) Monomeric crystal structure of the domain (PDB: 3T4L). The N-terminal dimerization domain, cytokinin-binding PAS-like domain, and C-terminal PAS-like domain are shown in blue, green, and orange, respectively. The ligand trans-zeatin is represented by red sticks, and the disulfide bridge is shown in pink. The disordered loop region is displayed by dotted line. (B) Cytokinin-binding pocket of AHK4. Trans-zeatin is represented by violet sticks. Active-site residues are shown as sticks in atomic colors (N, blue; O, red; C, green). Water molecules are shown by cyan spheres. Hydrogen bonds are shown as yellow dashes. Molecular Plant 2016 9, 71-85DOI: (10.1016/j.molp.2015.11.008) Copyright © 2016 The Author Terms and Conditions

Figure 3 Dimerization/Histidine Phosphotransfer Domain of ERS1. (A) Cartoon representation of the domain (PDB: 4MT8). Structures of the monomers are colored in a rainbow spectrum from N terminus (blue) to C terminus (red). The phosphate-accepting histidine residue and Met351 are shown as spheres. (B) Comparison of the topology of the hairpin loops of dimerization and histidine phosphotransfer domains of ERS1 (blue) and HK853 (red). Adapted from Mayerhofer et al., 2015. Molecular Plant 2016 9, 71-85DOI: (10.1016/j.molp.2015.11.008) Copyright © 2016 The Author Terms and Conditions

Figure 4 Cartoon Representation of the Catalytic/ATP-Binding Domain of ETR1, PDB: 4PL9. The structure is colored light brown. The N, G1, F, G2, and G3 boxes are colored violet, green, yellow, blue, and cyan, respectively. ADP is shown in stick form with atomic colors (blue for N, red for O, orange for P). Cadmium ions, chloride ion, and bonds coordinating chloride and cadmium ions are shown as light blue spheres, the green sphere, and yellow dashes, respectively. The disordered part of α5 is represented by dots. Molecular Plant 2016 9, 71-85DOI: (10.1016/j.molp.2015.11.008) Copyright © 2016 The Author Terms and Conditions

Figure 5 Superimposition of the Structures of the Receiver Domains of Arabidopsis Histidine Kinases. CKI1RD (yellow), ETR1RD (magenta), and AHK5RD (cyan) (PDB: 3MM4, 1DCF, and 4EUK, respectively). The root-mean-square deviation between CKI1RD and ETR1RD, CKI1RD and AHK5RD, and ETR1RD and AHK5RD is 1.6 Å for 117 aligned residues, 2.0 Å for 118 aligned residues, and 2.5 Å for 117 aligned residues, respectively. The red arrowhead depicts the position of loop β3-α3 in ETR1RD. Molecular Plant 2016 9, 71-85DOI: (10.1016/j.molp.2015.11.008) Copyright © 2016 The Author Terms and Conditions

Figure 6 Active Site of Receiver Domain of CKI1. Close-ups of ribbon diagrams of Mg2+- free (A) and Mg2+-bound (B) forms of the active site. Residues forming the active-site pocket are shown as sticks. Magnesium (Mg2+) ion and water are represented by spheres in magenta and cyan, respectively. The arrowheads highlight D1050 and K1105 side chains, revealing structural rearrangements upon magnesium binding. Molecular Plant 2016 9, 71-85DOI: (10.1016/j.molp.2015.11.008) Copyright © 2016 The Author Terms and Conditions

Figure 7 Cytoplasmic Portion of ETR1. (A) Schematic view of the cytoplasmic portion of the ETR1 receptor based on the best SAXS model published by Mayerhofer et al. (2015). Cytoplasmic domains of the dimeric receptor are represented by the cGMP-specific phosphodiesterase, adenylyl cyclase and FlhA domain (GAF, green), dimerization and histidine phosphotransfer domain (DHpD, blue), catalytic and ATP-binding domain (CAD, magenta), and receiver domain (RD, yellow). (B) Overall structure of bacterial HK853–RR468 complex (PDB: 3DGE). Bottom structure is created by 90° rotation of the upper structure around its horizontal axes. Color coding is the same as in (A). Molecular Plant 2016 9, 71-85DOI: (10.1016/j.molp.2015.11.008) Copyright © 2016 The Author Terms and Conditions

Figure 8 Cartoon Representation of AHP1, Isolated from Its Co-crystal Structure with AHK5, PDB: 4EUK. The structure is colored in a rainbow spectrum from blue (N terminus) to red (C terminus). The phosphate-accepting histidine residue is represented in stick form. Molecular Plant 2016 9, 71-85DOI: (10.1016/j.molp.2015.11.008) Copyright © 2016 The Author Terms and Conditions

Figure 9 Schematic Model of ARR10 DNA-Binding Motif and DNA Interaction. The structure of the ARR10 DNA-binding motif (PDB: 1IRZ) is colored in a rainbow spectrum from blue (N terminus) to red (C terminus). Molecular Plant 2016 9, 71-85DOI: (10.1016/j.molp.2015.11.008) Copyright © 2016 The Author Terms and Conditions

Figure 10 Cartoon Representation of AHP1 in Complex with the Receiver Domain of AHK5. AHP1 is shown in blue and AHK5 in green (PDB: 4EUK). Histidine and aspartate residues participating in phosphoryl group transfer and magnesium coordination are shown as yellow sticks. The magnesium ion is shown as a magenta sphere and the water molecule as a blue sphere. Molecular Plant 2016 9, 71-85DOI: (10.1016/j.molp.2015.11.008) Copyright © 2016 The Author Terms and Conditions