The N-terminal helix N1 packs against the nucleotide-specifying motif IV.

<p>The structures of FtsY in (A) apo form, (B) monomeric GMPPNP-bound form, (C) GMPPCP-bound form from the targeting complex with Ffh, and (D) monomeric GDP-bound form were aligned based on the P-loop; the N-domain (blue) and G-domain (green) are highlighted. In the structures of apo and GMPPNP-bound FtsY the N-terminal helix, N1 (cyan), extends into the N-domain and packs against the conserved GTPase motif IV which positions the nucleotide-specifying Asp258 to interact with the nucleotide. The α4 helix (yellow) anchors the interface between the N and G domains. The C-terminal helix, αC (red), which along with N1 pack together at the N/G interface, is observed in a similar arrangement in the three monomeric forms (A, B, D) but rearranges in the complex form of FtsY (C).</p

Structural adaptations in the active site upon nucleotide binding.

<p>(A) Asp258 is shown to progressively coordinate the nucleotide from the apo state to the Ffh-NG complex state. In F2 (magenta), the nucleotide is not coordinated by Asp258. In F1 (blue) the nucleotide is within weak coordinating distance to Asp258. In FtsY from the Ffh complex (green), Asp 258 coordinates the nucleotide (hydrogen bonds shown as dotted lines). (B) IBD residue Arg142 is shown to coordinate the magnesium ion and interact with the γ-phosphate in the complex form of FtsY (green). In F1 (blue) and F2(magenta), the ‘DTFRAGA’ motif unfolds and positions Arg142 out of the active site and away from interaction with the bound nucleotide. (C) In complex with Ffh-NG (green), the FtsY sidechains of Arg 195 and Asn111 are positioned out of the active site and away from the γ phosphate. In F1 (blue) and F2 (magenta), both Arg195 and Asn111 rotate towards the γ phosphate and the amino moiety of Asn111, now coordinating the γ phosphate in a non-canonical position.</p

Structure of FtsY apo/GMPPNP dimer from <i>Thermus aquaticus.</i>

<p>(A) Stereo view of the Cα backbone trace of FtsY apo/GMPPNP dimer (nucleotide not shown). The structure of FtsY is comprised of the N-terminal helix (residues 1–10), shown in cyan; the N-domain in blue; the G-domain in green; the insertion box domain (IBD) in gold and the conserved GTPase motifs (MI, MII, MII and MIV) in purple. (B) A ribbon diagram of the structure of FtsY in complex with non-hydrolyzable substrate analog GMPPNP crystallized in the presence of MgCl₂. No evidence for a coordinated Mg²⁺ ion was observed similar to the structure of GDP-bound FtsY <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0000607#pone.0000607-Padmanabhan1" target="_blank">[10]</a>. (C) A simulated annealing 2Fo–Fc omit map, contoured at 1σ, is shown. The bound GMPPNP was omitted. (D) Ribbon diagram of the structure of FtsY in complex with GMPPNP crystallized in the absence of MgCl₂. (E) A simulated annealing 2Fo–Fc omit map, contoured at 1σ with bound GMPPNP omitted. In the absence of Mg²⁺, the guanine and ribose moieties of the bound GMPPNP are less ordered than in the presence of MgCl₂ (C).</p

() Comparison between the structure of Ade2 and Cyt3 of our crystallization DNA (top) and Ade 441 and Ade 442 from the crystal structure of the 50S ribosomal subunit of (bottom)

<p><b>Copyright information:</b></p><p>Taken from "Crystal structure of the third KH domain of human poly(C)-binding protein-2 in complex with a C-rich strand of human telomeric DNA at 1.6 Å resolution"</p><p></p><p>Nucleic Acids Research 2007;35(8):2651-2660.</p><p>Published online 10 Apr 2007</p><p>PMCID:PMC1885661.</p><p>© 2007 The Author(s)</p> Hydrogen bonds are depicted as yellow dashed bars, atoms are color-coded light blue, red, grey, white and dark blue for nitrogen, oxygen, carbon, hydrogen and phosphorous, respectively. () Top: Overlay of the structure of Ade2 and Cyt3 of our crystallization DNA (red) and Ade 441 and Ade 442 from the crystal structure of the 50S ribosomal subunit of (blue). Bottom: Overlay of our DNA (red) and Ade2532 and Cyt 2533 from the crystal structure of the 50S ribosomal subunit of (blue)

Site-directed mutagenesis analysis of the role of selected active site residues on the steady-state kinetic parameters of NAD⁺ transformation catalyzed by bCD38.

a<p>Conversion of NAD⁺ into cADPR, in percent of the reaction products,</p>b<p>cADPR was determined using the cycling assay, the other data were obtained using a radiometric HPLC assay with ¹⁴C-NAD⁺ as substrate.</p

The Michaelis complex and the covalent intermediate trapped with the 2′-ribofluoro analog of NAD⁺.

<p>(A) Stereo view showing rFNAD non-covalently bound in the active site of the E218Q bCD38 mutant. Residues critical to substrate binding and catalysis are labeled. Hydrogen bonds are indicated with dashed lines. (B) Stereo view showing the rFNAD substrate covalently bound to residue Glu218 in the active site of the wt bCD38. Residues critical to substrate binding and catalysis are labeled. The water molecule hydrogen bonded to the N7 of the adenine ring and to the side chain of Glu138 is displayed as a red sphere. Hydrogen bonds are indicated with dashed lines. These two views highlight the conformational change undergone by the ligand from the ‘extended’ (A) to the ‘folded’ (B) conformation. The flipping of conserved residue Trp168 accompanies this ligand folding within the active site. (C) Superimposition of the rFNAD ligands observed in the Michaelis (yellow) and covalent (pink) complexes as shown in (A) and (B) respectively. This figure highlights the movement undergone by the adenosine moiety when progressing from the Michaelis complex to the covalent intermediate. The three views are in the same relative orientation.</p