DNA and RNA Modification Enzymes | Structure, Mechanism, Function and

Book

DNA and RNA Modification Enzymes

ABSTRACT

This volume is a timely and comprehensive description of the many facets of DNA and RNA modification-editing processes and to some extent repair mechanisms. Each chapter offers fundamental principles as well as up to date information on recent advances in the field (up to end 2008). They ended by a shortconclusion and future prospect' section and

TABLE OF CONTENTS

chapter |21 pages

Discovery of DNA Modification Enzymes

chapter |4 pages

Pro tein Inhibitors of Type I RM Systems

chapter |1 pages

Table 1. Base-flipping systems proven by crystal structures of protein-DNA complexes

chapter |59 pages

Table 1. Continued

chapter |6 pages

Acknowledgements

chapter |70 pages

Table DNA methylation and inherited disease

chapter |60 pages

hABHl

chapter |48 pages

Other Trans-Acting Factors

chapter |11 pages

Identification of the Gene Coding for the Flavoprotein TrmFO

chapter |1 pages

Multifunctional RNA Modification Enzymes

chapter |44 pages

Mode 1

chapter |27 pages

Splicing Endonuclease

chapter |46 pages

Table 2

Domain structure of enzymes of the six pseudouridine synthase families

chapter |6 pages

Tetrahydrofolate-Binding Fold

chapter |26 pages

References

chapter |3 pages

Structure, Function and Evolution o f Fibrillarin

chapter |6 pages

Acknowledgements References

chapter |3 pages

Additional Functions

chapter |25 pages

Ackn owledgements

chapter |7 pages

. Modified nucleosides explicitly involved in tRNA identity for aminoacylation

chapter |17 pages

Acknowledgements

chapter |6 pages

Conclusions and Future Prospects

chapter |5 pages

Figure 1, viewed on previous page. The nucleotide modification catalyzed by KsgA. A) The chemical reaction catalyzed by KsgA. The enzyme transfers a total of four methyl groups, two each to two adjacent adenosines. SAM is the methyl donor S-adenosylmethionine, while SAH is the product S-adenosyl homocysteine. The nucleotide numbers 1518 and 1519 refer to nucleotide numbering of the small subunit ribosomal RNA from E. coli. B) The secondary structure of 16S rRNA from E. coli is shown with helix 45 in expanded form. The nucleotides 1518 and 1519 are circled. The 16S rRNA secondary structure is from the Comparative RNA Web Site and Project (http://www.rna.ccbb.utexas.edu/) and is slightly modified for presentation here. Please refer to this site for an explanation of the 16S rRNA secondary structure and annotations.

chapter |4 pages

KsgA as a Ribosome Biogenesis Factor

chapter |10 pages

Conclusions and Future Prospects

chapter 2|4 pages

Aminoglycoside antibiotics

chapter |10 pages

Con clusion and Perspectives

chapter 3|17 pages

Different RNA Methyltransferases That Confer Orthosomycin Resistance

chapter |7 pages

Acknowledgements

chapter |10 pages

Bio chemical Analysis o f tRNA Degradation by the TRAM P Complex and Nuclear Exosome

chapter |1 pages

Figure 1. Phyletic patterns of conserved proteins from the three cellular Domains of life. Bacteria, Archaea and Eukarya are shown by large circles in a Venn diagram format. Homologous pro tein families are shown with either cross (unknown function) or circle (characterized function) symbols. PACE groups (in their senso stricto definition, i.e., absence in Bacteria) are marked in dark while other conserved proteins are in grey. The PACEs space is colored in dark grey.

chapter |3 pages

. PACEs current knowledge

chapter |7 pages

tRNA Maturation

chapter |2 pages

Figure 2. Protecting groups in standard phosphoramidites and selected phosphoramidites of modified nucleotides.

chapter |3 pages

Fig ure 4. Symbolism for protecting groups on the nucleoside.

chapter |2 pages

Figure 5. A) codon-anticodon interaction of mRNA and tRNA. B) kissing loop complex of a minimal construct S1 from Moloney murine leukaemia virus RNA and its wyosine containing model sequence offering a wider bases overlap. C) splint ligation approach to the synthesis of a minimal construct S2 containing wyosine (Y) at position 9. The DNA splint sequence (zigzag) contains an abasic site denoted

chapter |12 pages

Fig ure 6. Structures (symbolized) of proposed phosphoramidtes containing frequently used protecting groups.

chapter |13 pages

Tab le 2. Classification of enzymes in MODOMICS (December 2008). For each class, the number of enzymes and their ability to modify a certain nucleotide or its derivatives is given. The DSS in the rightmost column indicates enzymes having dual substrate specificity for different classes of RNAs, e.g.: tRNA and snRNA or tRNA and rRNA.

chapter |2 pages

References

chapter |7 pages

DNA Damage and Repair

chapter |1 pages

Table 1. Continued

chapter |1 pages

Table 7. Continued

chapter |1 pages

Table 2. DNA

chapter |1 pages

Table 3. Abbreviation list

chapter |4 pages

Table 4. Comments

chapter |3 pages

Table 2. Inhibitors and enzymatically inactive AdoMet analogs

chapter |1 pages

Databases on RNA and D NA M odification Enzymes

chapter |12 pages

RNA Sequences (see also RNA Structures and Motifs)