There is an uninterrupted chain between the nucleoplasm and the interior parts of the nucleolus, which occurs through a system of nucleolar passages. They are proposed to play any one or a combination of the following roles (Figure 5) (Jencks, 1969): (1) positioning the substrate and/or the attacking nucleophile; (2) enhancing the nucleophilicity of the phosphate at the scissile bond; (3) activating the nucleophile; (4) neutralizing the negative charge in the transition state; (5) facilitating the departure of the leaving group. The strand order is 32145, with strand 2 anti-parallel to the others. 6: 1096–1099, Goedken ER, Marqusee S . 1991 EMBO J. 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The binding modes of DNA nucleases are roughly divided into two categories, corresponding to non-specific and specific associations. The comparison of the free form with the complex revealed a small difference, suggesting that the surface of the enzyme contains a preformed pocket to be filled by the flipped out base. The nucleolus is not an organelle because it is devoid of a lipid membrane. 26: 3746–3752, Aravind L, Walker DR, Koonin EV . Previous sequence analyses have shown that this family includes RecJ and the phosphoesterases, which contain conserved phosphoesterase motifs (Aravind and Koonin, 1998a). The components can be further identified as: The ultrastructure of the nucleolus can be easily visualized through an electron microscope. 21: 3505–3515, Hamdan S, Carr PD, Brown SE, Ollis DL, Dixon NE . Representative repair nuclease of the folding is written in parenthesis. It then sends the subunits out to the rest of the cell where they combine into complete ribosomes. In eukaryotes, the gene coding for RNA contains a chain of at least 100-1000 repeating copies of DNA. 3: 364–376, Stewart GS, Maser RS, Stankovic T, Bressan DA, Kaplan MI, Jaspers NG, Raams A, Byrd PJ, Petrini JH, Taylor AM . 2001 Nucleic Acids Res. Similar ambiguity with respect to the number of metals was reported for RNaseHI, such as one magnesium (Katayanagi et al., 1993) and two manganeses (Goedken and Marqusee, 2001). APN1, the yeast homolog of E. coli endoIV, shows sequence and catalytic activity similarity to endoIV. In the NER pathway, a short stretch of DNA containing the damaged nucleotide is removed. Ribosomes make proteins; therefore, the nucleolus plays a vital role in making proteins in the cell. In eukaryotic cells, the nucleolus has a well-ordered structure with four main ultrastructural components. 2000 Nature 407: 711–717, Levin JD, Shapiro R, Demple B . α-helices are shown as blue cylinders.