Statistics of repetitive sequence.

<p>Statistics of repetitive sequence.</p

GC content and average sequencing depth of the genome data used for assembly.

<p>The x-axis was GC content percent across every 10-kb non-overlapping sliding window.</p

Statistics of gene information.

<p>Statistics of gene information.</p

Gene Ontology classification.

<p>Genes were assigned to three categories: cellular components, molecular functions, and biological process.</p

The proposed AsA synthetic and recycling pathways in higher plants.

<p>The four pathway included GalUA (D-galacturonic acid) pathway, Gal (L-galactose) pathway, Gulose(L-gulose) pathway and MI (Myo-inositol) pathway which catalyzed by GUR (D-galacturonate reductase), GME (GDP–D–Mannose-3,5-epimerase), GGP (GDP-L-galactose guanyltransferase), GPP (L-galactose-1-phosphate phosphatase), GDH (L-galactone dehydrogenase), GLDH (L-Galactono-lactone dehydrogenase) and MIOX(myo-inositol oxygenase). The recycling pathways were catalyzed by APX (ascorbate peroxidase), AAO (ascorbate oxidase), MDAR (mono-dehydroascorbate reductase) and DHAR (dehydroascorbate reductase).</p

Percentage of different mofits in dinucleotide repeats in <i>R</i>. <i>roxburghii</i>.

<p>Percentage of different mofits in dinucleotide repeats in <i>R</i>. <i>roxburghii</i>.</p

Statistics of sequencing data.

<p>Statistics of sequencing data.</p

Revelation of a Catalytic Calcium-Binding Site Elucidates Unusual Metal Dependence of a Human Apyrase

Human soluble calcium-activated nucleotidase 1 (hSCAN-1) represents a new family of apyrase enzymes that catalyze the hydrolysis of nucleotide di- and triphosphates, thereby modulating extracellular purinergic and pyrimidinergic signaling. Among well-characterized phosphoryl transfer enzymes, hSCAN-1 is unique not only in its unusual calcium-dependent activation, but also in its novel phosphate-binding motif. Its catalytic site does not utilize backbone amide groups to bind phosphate, as in the common P-loop, but contains a large cluster of acidic ionizable side chains. By employing a state-of-the-art computational approach, we have revealed a previously uncharacterized catalytic calcium-binding site in hSCAN-1, which elucidates the unusual calcium-dependence of its apyrase activity. In a high-order coordination shell, the newly identified calcium ion organizes the active site residues to mediate nucleotide binding, to orient the nucleophilic water, and to facilitate the phosphoryl transfer reaction. From ab initio QM/MM molecular dynamics simulations with umbrella sampling, we have characterized a reverse protonation catalytic mechanism for hSCAN-1 and determined its free energy reaction profile. Our results are consistent with available experimental studies and provide new detailed insight into the structure–function relationship of this novel calcium-activated phosphoryl transfer enzyme

Venn diagram showing the number of gene clusters in <i>R</i>. <i>roxburghii</i> and other close species, i.e., <i>M</i>.<i>×domestica</i>, <i>P</i>. <i>persica</i>, <i>P</i>. <i>bretschneideri</i>, and <i>P</i>. <i>mume</i>.

<p>The first number under the species name is the total number of putative genes subjected to clustering. The second number is the clustered family number. The overlapping areas represent sequences clustered with other species, and the number of non-overlapping areas represents specific genes.</p

K-mer (k = 17) analysis for estimating the genome size of <i>R</i>. <i>roxburghii</i>.

<p>The x-axis is depth (X); the y-axis is the proportion that represents the frequency at that depth divided by the total frequency of all depths. The genome size was estimated by using the formula: Genome size = K-mer num/Peak depth, and the heterozygosis rate causes a sub-peak at a position half of that of the main peak, whereas a certain repeat rate can cause a similar peak at the position of multiple integers of the main peak.</p