Structural and Biochemical Properties of Novel Self-Cleaving Ribozymes
<p>Secondary and tertiary structures of two representatives of twister ribozymes. (<b>A</b>) The structure of the twister ribozyme from <span class="html-italic">O. sativa</span> [<a href="#B30-molecules-22-00678" class="html-bibr">30</a>]. Additional stem-loop segments, P3 and/or P5, can be generated, as shown in black dotted lines; (<b>B</b>) The structure of the <span class="html-italic">env22</span> twister ribozyme [<a href="#B29-molecules-22-00678" class="html-bibr">29</a>]. In (<b>A</b>) and (<b>B</b>), red arrowhead indicates the U-A cleavage site. On the secondary structure, highly conserved nucleotides (>97%) are marked by asterisks. Stems (P1-P4) and pseudoknots (T1 and T2) are colour-coded in the tertiary structure. In particular, two nucleotides at the cleavage site and bound magnesium ions are coloured in cyan and yellow, respectively. Protein Data Bank (PDB) accession codes for (<b>A</b>) and (<b>B</b>) are 4OJI and 4RGE, respectively.</p> "> Figure 2
<p>Sequence and secondary structure model of the TS-1 twister sister ribozyme [<a href="#B9-molecules-22-00678" class="html-bibr">9</a>] (<b>A</b>) and the Ht-1 hatchet ribozyme [<a href="#B11-molecules-22-00678" class="html-bibr">11</a>] (<b>B</b>). Highly conserved and non-native nucleotides are coloured in red and grey, respectively. The cleavage sites are indicated by red arrowheads.</p> "> Figure 3
<p>Secondary and tertiary structures of the env25 pistol ribozyme [<a href="#B34-molecules-22-00678" class="html-bibr">34</a>]. On the secondary structure (<b>left</b>); highly conserved nucleotides are marked by asterisks, and red arrowhead indicates the G53-U54 cleavage site. Stems (P1-P3) and pseudoknots (T1) are colour-coded in the tertiary structure (<b>right</b>). In particular, two nucleotides at the cleavage site and bound magnesium ions are coloured in cyan and yellow, respectively. PDB accession code is 5K7C.</p> "> Figure 4
<p>Internal phosphoester transfer mechanism for RNA cleavage. The 2′ oxygen nucleophile of a sugar attacks its adjacent phosphorus atom, together with subsequent protonation and departure of the 5′ oxygen of a sugar.</p> ">
Abstract
:1. Introduction
2. Structures of the Novel Ribozymes
2.1. Twister Ribozyme
2.2. Twister Sister Ribozyme
2.3. Pistol Ribozyme
2.4. Hatchet Ribozyme
3. Insight into Catalytic Mechanisms of the Novel Ribozymes
3.1. Catalytic Strategies
3.2. Nucleobase Involvement in Catalysis
3.3. Metal Ion-Dependent Catalysis
4. Concluding Remarks
Acknowledgments
Conflicts of Interest
References
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Ribozyme Family | Alignment of O2′ to P-O5′ Bond (α Catalysis) | Neutralization of the Negative Charge on a Non-Bridging Oxygen (β Catalysis) | Deprotonation of 2′ Nucleophile (γ Catalysis) | Protonation of 5′ Leaving Group (δ Catalysis) | Cleavage Rate (min−1) at Neutral pH | Ref. |
---|---|---|---|---|---|---|
Twister 1 (O. sativa) | 83° (4OJI) | G45 | G45 | A7 | 2.45 | [30] |
Twister 1 (env9) | 83° (4QJH) | A63 | G62 | [28] | ||
Twister 1 (env22) | 148° (4RGE) | G48, Mg2+ | G48? 2 | A6? 2 | 2.44 (at 20 °C) | [29,31] |
91° (5DUN) | Mg2+-bound water? 2 | 1.41 (at 15 °C) | ||||
Pistol | 167° (5K7C) | G40 | G40 | A32 (or G32) | 2.72 (at 20 °C) | [34,35] |
126° (5KTJ) | 0.88 (at 15 °C) | |||||
HDV | 140° (5DI2) | Mg2+ | Mg2+ | C75 | 52 | [60,61] |
Hammerhead | G12 | G8, metal-bound water | 1.39 | [46,62] | ||
Hairpin | G8 | G8 | A38 | 0.1–0.5 | [63,64] | |
Neurospora VS | G638 | G638 | A756 | 1 | [23,65] | |
glmS | GlcN6P | G40 | GlcN6P | 1–3 | [26,48] |
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Lee, K.-Y.; Lee, B.-J. Structural and Biochemical Properties of Novel Self-Cleaving Ribozymes. Molecules 2017, 22, 678. https://doi.org/10.3390/molecules22040678
Lee K-Y, Lee B-J. Structural and Biochemical Properties of Novel Self-Cleaving Ribozymes. Molecules. 2017; 22(4):678. https://doi.org/10.3390/molecules22040678
Chicago/Turabian StyleLee, Ki-Young, and Bong-Jin Lee. 2017. "Structural and Biochemical Properties of Novel Self-Cleaving Ribozymes" Molecules 22, no. 4: 678. https://doi.org/10.3390/molecules22040678
APA StyleLee, K. -Y., & Lee, B. -J. (2017). Structural and Biochemical Properties of Novel Self-Cleaving Ribozymes. Molecules, 22(4), 678. https://doi.org/10.3390/molecules22040678