Three-dimensional structure prediction of the SHOCT domain of UniProtKB B0PET9.1 (residues 20–50) generated with QUARK using the default parameters[<b>12</b>] and viewed using MarkUs [<b>44</b>].

<p>Surface electrostatic potential for the model is calculated using the program GRASP2 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057848#pone.0057848-Petrey2" target="_blank">[45]</a> accessed through MarkUs. The positively charged areas of the protein surface are shown in blue, and negatively charged areas in red, the two alpha helices are overlaid in grey.</p

Histogram showing the bit scores distribution of the SHOCT domain HMM compared to a reversed version of the SHOCT domain HMM, searched against the UniProtKB database.

<p>The UniProtKB database was searched using an HMM constructed from the SHOCT seed alignment (unfilled bars) and an HMM from the reversed version of this alignment (green bars). The vertical line represents the sequence inclusion threshold.</p

The SHOCT peptide does not multimerise the rat Cd4d3+4 protein.

<p>(<b>A</b>) Tissue culture supernatants containing biotinylated Cd4d3+4-F0QBY7.1 and Cd4d3+4-F0QBY7.1_shuffled were resolved by SDS-PAGE under reducing conditions, blotted and detected using streptavidin-HRP. (<b>B</b>) Purified Cd4d3+4-F0QBY7.1 and Cd4d3+4-F0QBY7.1_shuffled were resolved on a Superdex 2000 Tricorn 10/600 column. The elution volumes of protein standards are marked in red. The expected monomer size for Cd4d3+4-peptide is 33 kDa. (<b>C</b>) Purified Cd4d3+4-F0QBY7.1 and Cd4d3+4-F0QBY7.1_shuffled were resolved by SDS-PAGE under non-reducing conditions before (Ni) and after size exclusion chromatography (SE) and detected Coomassie Brilliant Blue R-250 staining.</p

Domain architectures of selected proteins containing the SHOCT domain.

<p>Panel a shows proteins which are likely to be oligomeric, panel b shows enzymes and panel c shows binding proteins. Signal peptide and transmembrane domains are predicted using the Phobius web server <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057848#pone.0057848-Kall1" target="_blank">[46]</a>.</p

2D [¹⁵N,¹H] HSQC spectra of lipoprotein YxeF.

<p>(A) Spectrum recorded for the sample used for NMR structure determination at 750 MHz ¹H resonance frequency. Resonance assignments are indicated using the one-letter amino acid code. Signals arising from side chains (Asn H^δ2/N^δ2, Gln H^ε2/N^ε2, Arg H^ε/N^ε and Trp H^ε1/N^ε1) are labeled with (*) and folded signals are designated with (†) next to the residue number. Signals arising from the His purification tag were not sequence specifically assigned. The spectral region indicated by dotted lines comprises most of the signals arising from the β-barrel (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037404#pone-0037404-g002" target="_blank">Figure 2</a>) and is displayed for the spectra shown in (B). Those were recorded at different temperatures at 500 MHz ¹H resonance frequency (see text).</p

Comparison of β-barrels.

<p>Ribbon drawings of β-barrels of avidin (PDB ID 1AVD, green) in (A) and, after rotation by 180°, in (D); bacterial lipocalin Blc from <i>E. coli</i> (PDB ID 3MBT, orange) in (B) and (E); YxeF in (C) and (F) (PDB ID 2JOZ, blue). For clarity, the disordered terminal polypeptide segments of YxeF, as well as the corresponding segments in avidin and Blc, are not shown. In (A)–(C), β-strands A and H are labeled, while in (D)–(F) β-strand D is indicated.</p

Schematic representation of secondary structure element topologies.

<p>(A) YxeF, (B) lipocalins and (C) fatty acid-binding proteins. β-strands are represented by arrows, α-helices by rectangles, and 3₁₀-helices by ellipses. N- and C-termini are indicated as N and C respectively, and the ‘Ω-type’ loop L1 shared by YxeF and lipocalins is labeled.</p

Statistics of YxeF(19–144) NMR Structure.

a<p>Relative to pairs with non-degenerate chemical shifts.</p>b<p>Residues 37–40, 53–58, 62–69, 73–76, 80–86, 92–98, 105–110, 116–120, and 123–128.</p>c<p>Residues 33–40, 45–48, 51–87, 93–96, 99–101, 104–111, 115–131.</p>d<p>Backbone and side-chain heavy atoms of residues 37–39, 54–59, 63–64, 66, 68, 75, 77, 81–82, 84–86, 93–96, 98, 105–108, 115–118. Best-defined side chains are those exhibiting a displacement of less than 1 Å for their side chain heavy atoms after superposition of the β-strands for minimal r.m.s.d.</p

Comparison of YxeF NMR structure (PDB ID 2JOZ, coded in blue) and Blc X-ray crystal structure (PDB ID 3MBT, orange).

<p>(A) Structure-based sequence alignment between YxeF and Blc obtained with the program DALI <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037404#pone.0037404-Holm1" target="_blank">[16]</a>. The three structurally conserved regions (SCR1-3) typically found in lipocalins (see text) are boxed (continuous line for SCR1, which appears to be conserved in YxeF; dashed line for SCR2 and SCR3). Conserved residues being part of the calycin signature motif resulting in an interaction between Gly 36-X-Trp 38 in SCR1 and Arg 128 in SCR3 (see text) are highlighted using red boxes. Residues being part of the second hydrophobic core of Blc [see also (D] are highlighted using cyan boxes. (B) Superposition of the Trp and Arg residues being part of the calycin Gly-X-Trp and Arg motif in Blc (licorice representation, orange) and YxeF (line representation, all NMR conformers, blue). The superposition is obtained after superposition of the X-ray structure of Blc with each conformer of the NMR solution structure of YxeF (residues 32–132). (C) Structural superposition generated by the program DALI viewed from the open end of the β-barrels (for YxeF residues 32–132 were considered). In Blc, box 1 identifies the C-terminally located α-helix and box 2 the C-terminal β-strand, which are packed against the outside of the β-barrel and thereby form a second hydrophobic core (see D). (D) Ribbon drawing of the Blc structure with licorice representation of hydrophobic residues (in cyan) located in the C-terminal α-helix and on the outside of the β-barrel forming a second hydrophobic core [see also (C)].</p

Comparison of <i>B. subtilis</i> YxeF NMR structure and <i>B. amyloliquefaciens</i> A7ZAF5 homology model.

<p>Surface electrostatic potential calculated for (A) the YxeF NMR structure (first conformer of ensemble deposited in the PDB) and (B) the homology model of A7ZAF5 by using the program GRASP <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037404#pone.0037404-Petrey2" target="_blank">[56]</a> accessed through the protein function annotation server MarkUs <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037404#pone.0037404-Petrey1" target="_blank">[55]</a>. The homology model was calculated using the SWISS-MODEL server in alignment mode <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037404#pone.0037404-Altschul1" target="_blank">[60]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037404#pone.0037404-Arnold1" target="_blank">[61]</a> and Verify3D <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037404#pone.0037404-Luthy1" target="_blank">[63]</a>, Procheck <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037404#pone.0037404-Laskowski1" target="_blank">[64]</a> and ProsaII <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037404#pone.0037404-Sippl1" target="_blank">[65]</a> all atom z-scores (-1.12, −3.43 and −1.61, respectively) were obtained using the PSVS server <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037404#pone.0037404-Bhattacharya2" target="_blank">[66]</a> and are indicative of a good quality model. In (C) and (D), ribbon drawings are shown for the structures of YxeF and A7ZAF5 in the same orientation, that is, viewed on the open end of the β-barrels. The acidic residues giving rise to the negative potential inside the cavities are depicted in licorice representation and are labeled (black for YxeF, red for A7ZAF5). (E) Pfam multiple alignment of the sequences of all members of PF11631. Except for YxeF (P54945), the sequences are labeled with their UniProt <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037404#pone.0037404-UniProt1" target="_blank">[25]</a> IDs (D4G3V0, E8VFY0, E0TYE6, D5MWC1, E3E109, A7ZAF5, E1UTS8). Amino acid background colors reflect average similarity inferred from the Blosum62 matrix, ranging from ‘most conserved’ (black) to ‘least conserved’ (white). YxeF and A7ZAF5 are highlighted in bold on the left and the region of the alignment used for building the comparative model of A7ZAF5 from the YxeF structure is enclosed by red boxes. The acidic residues labeled in (C) and (D) are marked with black (YxeF) and red (A7ZAF5) asterisks, respectively, above or below the alignment.</p