Functional and Structural Models of Group I Intron Active Sites

<div><p>(A) Model of the <i>Tetrahymena</i> ribozyme transition state from functional data with the C262 <i>pro</i>-<i>S</i>_P phosphoryl oxygen and C208 <i>pro</i>-<i>S</i>_P oxygen coordinating to M_C and M_A, respectively ([<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030277#pbio-0030277-b35" target="_blank">35</a>,<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030277#pbio-0030277-b36" target="_blank">36</a>,<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030277#pbio-0030277-b53" target="_blank">53</a>,<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030277#pbio-0030277-b58" target="_blank">58</a>,<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030277#pbio-0030277-b71" target="_blank">71</a>,<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030277#pbio-0030277-b72" target="_blank">72</a>, <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030277#pbio-0030277-b74" target="_blank">74</a>], data herein, and AVK, JLH, JAP, and DH, unpublished results).</p> <p>(B) Model of Mg²⁺ binding in the crystal structure of a thermostable variant of the <i>Tetrahymena</i> group I ribozyme (derived from PDB file 1X8W) [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030277#pbio-0030277-b14" target="_blank">14</a>]. The model shown is derived from molecule C, although the position of the metal ion appears to vary among the four molecules observed in the asymmetric unit. The putative Mg²⁺ ion (dashed green circle) is 2.4 Å from the <i>pro-S</i>_P oxygen of C262 and 2.1 Å from the terminal G (ωG) 2′-OH. U(-1) is not shown, as the crystallized form of the thermostable <i>Tetrahymena</i> variant ribozyme lacks this nucleotide.</p> <p>(C) Model of K⁺ binding from the crystal structure of the <i>Azoarcus</i> group I ribozyme (derived from PDB file 1T42) [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030277#pbio-0030277-b15" target="_blank">15</a>]. The putative K⁺ ion (dashed green circle) is 2.4 Å from the <i>pro-S</i>_P oxygen of G128 (C262 homologue) and 2.8 Å from the modeled position for the terminal G (ωG) 2′-OH; the <i>Azoarcus</i> intron construct that was crystallized contained 2′-deoxyguanosine at ωG, and electron density for the K⁺ ion is observed only in the presence of this 2′-deoxyguanosine modification at ωG.</p> <p>(D) Model of proposed Mg²⁺ binding site derived from the crystal structure of the Twort group I ribozyme [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030277#pbio-0030277-b13" target="_blank">13</a>]. The crystallographic data lack clear density for a metal ion in the region expected for the M_C binding site but show the <i>pro</i>-<i>S</i>_P phosphoryl oxygen of A120 (C262 homologue) and the 2′-OH of ωG appropriately juxtaposed to coordinate a single Mg²⁺ ion (purple circle).</p>