S-adenosylmethionine-dependent Methyltransferases

Structures And Functions

By: Robert M Blumenthal (Editor), Xiaodong Cheng (Editor)

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Hardcover | 27 July 1999

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This invaluable volume, written by an international group of scientists, presents an overview of the AdoMet-dependent methyltransferases, with special emphasis on structure-function relationships.S-adenosyl-L-methionine (AdoMet) is the second most commonly used enzyme cofactor after ATP. The AdoMet-dependent methyltransferases act on a wide variety of target molecules, including DNA, RNA, protein, polysaccharides, lipids and a range of small molecules.The well-conserved architecture of these enzymes, and the implications of this conservation for their evolutionary history, are major themes of this book. The thirteen chapters describe in detail the structures, enzyme kinetics and biological roles of the AdoMet-dependent methyltransferases from a wide range of cell types: plant, animal, bacterial and archaeal.

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Non-Fiction Science Biology, Life Sciences Biochemistry Enzymology Physics Engineering & Technology Biochemical Engineering Cellular Biology Booktopia Publisher Services World Scientific Publishing

Structure and Evolution of AdoMet-Dependent Methyltransferases	p. 1
Introduction: chemistry of AdoMet-dependent methyltransfer	p. 1
AdoMet is a very commonly-used cofactor	p. 1
Various types of AdoMet-dependent methylation	p. 3
Chemistry of methylating different atoms	p. 6
A common architecture for AdoMet-dependent MTases	p. 8
Almost all examples solved to date share a common core	p. 8
AdoMet binding	p. 15
Conserved amino acid sequence motifs	p. 17
A relationship between the AdoMet-dependent MTases and the Rossmann fold proteins	p. 20
The overall architecture of AdoMet-dependent MTases is strikingly similar to that of the eight known families of Rossmann fold proteins	p. 20
The positions of the adenosine moieties of Rossmann fold proteins are exactly analogous to the positions of the AdoMet adenosine moieties in the MTases	p. 21
Catalytically-active sidechains occupy some analogous and some distinct positions in AdoMet-dependent MTases and Rossmann fold proteins	p. 23
Did the MTases arise from gene duplication?	p. 24
Classification of MTases: overall sequence similarity vs. motif order	p. 25
Structure-guided alignments reveal a low degree of overall sequence conservation	p. 25
Variation in linear motif order among MTases	p. 25
Does the structural conservation among AdoMet-dependent MTases reflect divergent or convergent evolution?	p. 27
Criteria for distinguishing divergent from convergent evolution	p. 27
Divergence of the [beta] family of DNA MTases might be explained by derivation from a circularly-permuted RNA MTase	p. 29
Conclusions and future work	p. 30
Acknowledgements	p. 30
References	p. 32
The Black Sheep of the Family: AdoMet-Dependent Methyltransferases that do not Fit the Consensus Structural Fold	p. 39
Introduction	p. 39
Reactivation domain of cobalamin-dependent methionine synthase (MetH)	p. 40
Role of the MetH reactivation domain	p. 40
Structure of MetH reactivation domain	p. 43
Conformation and interactions of AdoMet in the MetH reactivation domain	p. 44
Reaction with the cobalamin-binding domain	p. 45
Precorrin MTase CbiF	p. 46
Role of CbiF	p. 46
Structure of CbiF	p. 46
Interactions and conformation of AdoHcy bound to CbiF	p. 48
AdoMet/AdoHcy binding in catechol-O-MTase, MetH and CbiF	p. 50
Perspectives	p. 51
Acknowledgements	p. 52
References	p. 52
Catechol O-Methyltransferase	p. 55
Introduction	p. 55
S-COMTase and MB-COMTase enzyme forms	p. 56
Distribution of COMTase proteins in mammalian tissues	p. 57
Subcellular localization of COMTase proteins	p. 58
COMTase gene	p. 60
Structure of COMTase gene	p. 60
Regulation of COMTase expression	p. 61
Genetic polymorphism of human COMTase	p. 61
Enzyme kinetic mechanisms	p. 63
Kinetics of COMTase polymorphs with different thermostability	p. 64
Crystal structures of COMTase	p. 65
Structure of COMTase complexed with AdoMet, 3,5-dinitrocatechol and magnesium	p. 66
The active site--AdoMet binding and magnesium binding	p. 66
Binding of catechol-like structures of COMTase	p. 69
Species-related active site differences	p. 69
Structure of COMTase complexed with OR-1840	p. 70
Reaction mechanism of the methyltransfer catalyzed by COMTase	p. 72
Inhibition of the COMTase enzyme	p. 75
New COMTase inhibitors	p. 75
Inhibition mechanism of nitrocatechol-type inhibitors	p. 77
Practical clinical applications and theoretical indications of COMTase inhibitors	p. 77
COMTase inhibitors as an aid in positron emission tomography (PET)	p. 79
References	p. 80
Glycine N-Methyltransferase, A Tetrameric Enzyme	p. 93
Introduction	p. 93
GNMTase	p. 94
Physicochemical properties of rat liver GNMTase	p. 95
Amino acid sequence of GNMTase	p. 95
Kinetic properties of GNMTase	p. 96
Inactivation of GNMTase by chemical modification	p. 100
Crystal structure of rat GNMTase	p. 101
Tetramer structure	p. 102
AdoMet binding site	p. 104
Chemical mechanism of GNMTase reaction	p. 106
Folate binding to GNMTase	p. 109
Comparison to the structure and function of AdoHcy hydrolase	p. 111
Relationship between GNMTase and AdoHcy hydrolase	p. 112
Tissue and subcellular localization, and physiological role of GNMTase	p. 114
Future work	p. 117
References	p. 119
A Protein Carboxyl Methyltransferase that Recognizes Age-Damaged Peptides and Proteins and Participates in their Repair	p. 123
Introduction	p. 123
Distribution of the L-isoaspartyl MTase in nature	p. 124
Structure of the L-isoaspartyl MTases	p. 127
Genes specifying L-isoaspartyl MTases	p. 127
Diversity of mammalian enzymes due to alternative splicing of transcripts and gene polymorphisms	p. 128
Enzyme structure and localization	p. 129
Availability of purified enzymes	p. 129
Three-dimensional structural studies	p. 129
Substrate specificity of the MTase	p. 131
Are some proteins more prone to isomerization and racemization than others?	p. 132
Alternative sources of L-isoaspartate residues in proteins	p. 132
Repair pathways	p. 134
Repair of D-aspartate residues?	p. 134
Repair of extracellular proteins?	p. 134
Self-repair of L-isoaspartyl MTase	p. 135
Defective repair in human diseases	p. 135
A role for repair in proteolysis?	p. 135
Gene knockout model systems for studying the physiological role of the L-isoaspartyl MTase	p. 136
Bacteria	p. 136
Yeast	p. 137
Worms	p. 137
Flies	p. 138
Amphibians	p. 138
Mice	p. 138
Plants	p. 139
Future work	p. 139
Acknowledgements	p. 139
References	p. 140
Protein Methyltransferases Involved in Signal Transduction	p. 149
Introduction	p. 149
Bacterial Receptor MTases	p. 150
Receptor methylation	p. 150
Structure of MTase CheR	p. 152
MTase-receptor interactions	p. 154
Sequence analysis	p. 159
Prenylcysteine MTases	p. 160
CAAX-tail processing	p. 160
Enzymology of the prenylcysteine methylation system	p. 162
Prenylcysteine MTase substrates and inhibitors	p. 165
Function of prenylcysteine methylation	p. 165
Phosphoprotein phosphatase 2A MTases	p. 166
Phosphoprotein phosphatase 2A	p. 166
PP2A MTase	p. 167
PP2A methylesterase	p. 168
Protein arginine MTases	p. 168
Arginine methylation	p. 168
Involvement in signaling	p. 170
Sequence analysis	p. 172
Acknowledgements	p. 172
References	p. 173
tRNA Methyltransferases	p. 185
Introduction	p. 185
Biological function	p. 185
Classes of enzyme	p. 186
tRNA 5mU54 MTase (RUMT)	p. 187
tRNA N1mG MTase (1MGT)	p. 189
tRNA mG18 2'-O-MTase	p. 192
tRNA 5mC MTase	p. 192
tRNA N1mA58 MTase	p. 193
tRNA N2,2mG26 MTase	p. 193
Summary and Conclusions	p. 193
References	p. 194
rRNA Methyltransferases (ErmC' and ErmAM) and Antibiotic Resistance	p. 199
Introduction	p. 199
MTases involved in rRNA processing and maturation	p. 201
General considerations about rRNA MTases	p. 201
rRNA MTases modifying ribose sugars	p. 202
rRNA MTases modifying nucleotide bases	p. 203
rRNA MTases involved in antibiotic resistance	p. 204
General considerations	p. 204
Macrolide-Lincosamide and streptogramin-B resistance: Erm rRNA MTases	p. 205
Structures of ErmC' and ErmAM	p. 206
Consensus structure of the Erm family of rRNA MTases	p. 208
Structural relation to N6mA DNA MTases	p. 208
AdoMet binding	p. 210
rRNA recognition	p. 211
Structure-guided amino acid sequence comparisons among rRNA MTases	p. 214
tRNA MTases	p. 217
Conclusions and future work	p. 218
Acknowledgements	p. 218
References	p. 218
Nucleoside Methylation in Eukaryotic mRNA: HeLa mRNA (N6-Adenosine)-Methyltransferase	p. 227
Introduction	p. 227
Methylated nucleosides present in eukaryotic mRNA--the 5'-terminal cap structure	p. 227
Biological function of methylated nucleosides within the cap structure	p. 228
Enzymes involved in cap methylation	p. 228
Modified nucleosides at internal positions in eukaryotic mRNA	p. 229
N6mA	p. 230
Sequence specific distribution of N6mA in vivo	p. 231
Function of N6mA in mRNA	p. 232
Mutation of N6mA sites	p. 232
Studies utilizing methylation inhibitors	p. 233
Characterization and purification of HeLa mRNA N6mA MTase	p. 235
Sequence specificity in vitro	p. 235
Purification of HeLa mRNA N6mA MTase	p. 237
Purification and cDNA cloning of the AdoMet-binding subunit	p. 238
GenBank and Expressed Sequence Tag (EST) database homology searches	p. 238
Northern blot analysis of MT-A70 expression	p. 244
Subnuclear localization of MT-A70 in HeLa Cells	p. 245
Further characterization of MT-B	p. 246
Conclusion	p. 247
References	p. 247
VP39--An mRNA Cap-Specific 2'-O-Methyltransferase	p. 255
Introduction	p. 255
mRNA biogenesis: outline of terminal processing steps	p. 255
Vaccinia as an enzymological tool	p. 256
Vaccinia protein VP39--a nucleic acid ribose MTase and a poly(A) polymerase processivity factor	p. 256
VP39 overall architecture and evolution	p. 257
Architecture	p. 257
Relationship to other AdoMet-dependent MTases	p. 258
Cofactor	p. 259
AdoMet binding mutants	p. 259
VP39-AdoMet interactions	p. 261
AdoMet-binding mutant phenotypes in a structural context	p. 262
N7mG moiety of the mRNA cap	p. 262
Specificity	p. 262
Cap-dependent RNA binding assay based on surface plasmon resonance	p. 263
N7mG-binding pocket	p. 264
VP39-N7mG interactions	p. 264
Reconciling the mutagenesis and crystallography	p. 265
How does VP39 discriminate 7-methylated from unmethylated G?	p. 266
How might the Y22/F180 stacking sandwich favor 7-methylated over unmethylated G?	p. 268
By what biophysical mechanism might the positively charged N7mG base enhance stacking?	p. 268
Adenine-cap binding to the N7mG pocket in the context of capped RNA	p. 269
Hydrogen-bonding to N7mG	p. 269
MTase-specific VP39-RNA interactions: A four-site model for VP39-substrate interaction	p. 270
Downstream RNA-binding cleft	p. 270
VP39-phosphoribose backbone interactions within minimal MTase substrates	p. 272
pH-dependent binding of the first RNA trimer	p. 273
A distal downstream RNA-binding site?	p. 275
Basic enzymology and possible catalytic mechanism	p. 275
Interaction between VP39's two functions	p. 277
Conclusions and future work	p. 278
References	p. 279
Bacterial DNA Methyltransferases	p. 283
Introduction	p. 283
The DNA MTases	p. 283
Base flipping	p. 283
Scope of this chapter	p. 284
Biology of DNA MTases	p. 285
Dam and Dcm MTases	p. 285
R/M systems	p. 286
Antirestriction MTases	p. 287
Structural domains	p. 288
Target recognition domains (TRDs)	p. 288
AdoMet binding and catalytic domain	p. 291
Other domain structures	p. 291
Endonuclease DNA cleavage domains	p. 292
DNA helicase domains	p. 293
Classification of DNA MTases	p. 295
Type II R/M systems	p. 295
Type IIs R/M systems	p. 296
Multifunctional MTases	p. 296
Type I R/M system	p. 296
Specificity (S) subunits	p. 297
Modification (M) subunits	p. 300
Restriction (R) subunits	p. 301
Type I 1/2 R/M systems	p. 302
BcgI-like R/M systems	p. 302
Type III R/M systems	p. 303
Type IV R/M systems	p. 304
Assembly of DNA MTases	p. 305
Chemical reactions of DNA MTases	p. 306
5mC methylation	p. 306
N4mC and N6mA methylation	p. 308
Kinetics of DNA methylation	p. 309
Physical mechanism	p. 310
Locating the DNA target sequence	p. 310
DNA binding affinity	p. 311
DNA footprinting	p. 313
Type II MTases	p. 313
DNA bending by type II MTases	p. 313
Footprinting of type I R/M enzymes	p. 314
Substrate-induced conformational changes in DNA MTases	p. 314
Crystallographic evidence	p. 314
Limited proteolysis of MTases	p. 315
Spectroscopic methods	p. 316
Hydrodynamic measurements	p. 316
Conformational changes in the DNA and nucleotide base flipping	p. 317
Mechanism of EcoRI N6mA MTase	p. 319
Summary	p. 319
Acknowledgements	p. 321
References	p. 321
Eukaryotic DNA Methyltransferases	p. 341
Introduction	p. 341
Establishment of genome methylation patterns	p. 341
Enzymology of Eukaryotic MTases	p. 343
Eukaryotic DNA MTase familes	p. 345
Dnmt1 family MTases	p. 349
Substrate selectivity	p. 351
Dnmt1: single gene or multigene family?	p. 353
Maintenance methylation and DNA replication	p. 354
De novo methylation by Dnmt1	p. 356
Dnmt2 family MTases	p. 357
Yeast DNA MTases?: pmt1	p. 358
Masc-1 family DNA MTases	p. 359
Dnmt3 family MTases	p. 359
MTases and chromatin structure: TrxG/PcG proteins, methylated DNA binding proteins and chromomethylases	p. 360
Conclusion	p. 361
Acknowledgements	p. 362
References	p. 362
Mechanisms of DNA Demethylation in Vertebrates	p. 373
Introduction	p. 373
DNA methylation/demethylation and the formation of methylation patterns	p. 374
Passive demethylation	p. 375
Natural inhibitors of DNA MTase	p. 376
Nucleotide analogs as inhibitors of DNA methylation	p. 376
Passive demethylation by drugs influencing the level of AdoMet	p. 377
Active demethylation	p. 378
Indirect evidence for the presence of an active DNA demethylation system	p. 378
Direct evidence for active DNA demethylation	p. 379
5mC-DNA glycosylase	p. 380
The activity of 5mC-DNA glycosylase requires both protein and RNA	p. 381
RNA alone is causing DNA demethylation	p. 382
Cis-trans regulatory elements of DNA demethylation	p. 383
Sequence of events leading to site specific demethylation of the avian vitellogenin gene	p. 384
Conclusions and future work	p. 385
Acknowledgements	p. 385
References	p. 385
Appendix I	p. 393
Appendix II	p. 398
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S-adenosylmethionine-dependent Methyltransferases

Structures And Functions

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