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Catalysis and regulation
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Catalysis and regulation Editorial overview Thomas Carell Current Opinion in Structural Biology 2012, 22: 689–690 For a complete overview see the Issue Available online 8th November 2012 0959-440X/$ – see front matter, # 2012 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.sbi.2012.10.006
Thomas Carell Department of Chemistry, LudwigMaximilians-Universita¨t (LMU), Butenandtstr. 5-13 (Haus F), Mu¨nchen D-81377, Germany e-mail: [email protected] Thomas Carell is a professor for Organic Chemistry to the Ludwig-MaximiliansUniversita¨t (LMU) in Munich (Germany). The Carell Group is a research group concentrating on nucleic acid chemistry at the Ludwig-Maximilians-Universita¨t Mu¨nchen. Our projects present a wide variety throughout the field including, for example, DNA damage and repair, DNA modifications in epigenetics and click chemistry. To achieve our goals we combine classical organic synthesis with protein biochemistry.
Standard biochemistry textbooks depict in those sections where DNA and RNA are discussed the four Watson Crick bases and they show the 20 standard, canonical, amino acids as the central building block of proteins. We know for a long time that this view is far too simple. All biomolecules including proteins and nucleic acids are often heavily modified posttranslationally and the underlying modification chemistry goes far beyond simple phosphorylations of serine and threonine residues or the ubiquitinylation of proteins needed to tag them for degradation. We understand today that the reversible methylation, acetylation, malonylation, crotonylation or even citrullinylation, to name just a few, of key lysine residues, for example, in histone tails, establish a type of epigenetic genetic code that goes beyond the sequence code. On the DNA level we see that the cytosine residues are either methylated (mC), hydroxymethylated (hmC), formylated (fC) or carboxylated (caC) at position C5 and while we have a good picture of the biological function of mC, the functional role of all the other newly discovered dC-modifications remains to be elucidated. We are learning that radical enzymes are of key importance to manipulate the canonical bases and amino acids in order to establish or erase the modifications discussed above. As such they are essential for establishing a reversible modification chemistry that encodes (epigenetic)-information that we are just beginning to decipher. In the whole field of posttranslational modifications we find the radical SAM enzymes in essential positions. They employ complex chemistry and control highly reactive intermediates in order to allow manipulation of the canonical biomolecules. a-Ketoglutarate-dependent oxidases activate oxygen and they split the oxygen molecule in order to transfer one oxygen atom to the substrate. The other oxygen atom is used to perform the simultaneous oxidative decarboxylation of the co-substrate a-ketoglutarate. Enzymes using this chemistry are responsible for the formation of the mentioned dC-derivative hmC, fC and caC, which are believed to be essential for correct cellular development. In this context a-ketoglutarate oxidizes in TET1-3 the substrate mC in a stepwise fashion to first hmC and then fC and caC. Other a-ketoglutarate enzymes are essential for the demethylation of trimethylated lysine residues in histone tails. Mono-methyllysine and di-methyllysine residues (–NMe1/2) can be quickly oxidized with flavin-dependent oxidases. The key step is a single electron transfer from the amine lone pair to the flavin cofactor bound in the enzyme followed by a loss of a proton to give an imine intermediate. This subsequently hydrolyses in the aqueous environment to give formaldehyde and the demethylated amine. This type of chemistry can, however, not be employed for the demethylation of trimethyllysine residues (–N+Me3), which lack the electron donating N-lone pair. Here aketoglutarate-dependent oxidizations are again needed, which convert one
www.sciencedirect.com
Current Opinion in Structural Biology 2012, 22:689–690
690 Catalysis and regulation
of the methyl groups into a hydroxymethyl moiety thereby creating an N,O-acetal [–N(Me)CH2OH], which hydrolyzes quickly. Christopher Schofield gives in his review an overview about this interesting class of proteins and summarized — based on recent crystal structures — the structural prerequisites that enable the proteins control of the complex radical-based oxidation chemistry. Other radical enzymes that are involved to establish posttranslational modification are 4Fe/4S-cluster containing SAM enzymes, which, for example, transfer methyl groups to RNA bases in order to create methylated noncanonical bases within RNA. Here a reductase first reduces and thereby activates the 4Fe/4S cluster, which subsequently donates an electron to the S-adenosylmethionine cofactor/cosubstrate (SAM) converting it into the highly reactive 5-adenosylradical. This elusive species can either initiate the reaction directly by abstracting an H-atom from the substrate or alternatively, it abstracts an H-atom from a nearby glycine residue creating a glycine radical, which then acts as a resting state for the protein. In these enzymes, it is the glycine radical which initiates catalysis by H-atom transfer from the substrate. Most recently it was discovered that some of the radical-SAM enzymes, involved, for example, in the methylation of adenine residues at position C(3), use two SAM molecules during catalysis. One is needed to start the radical chemistry while the second SAM molecule donates the methylgroup as a Me+-equivalent. These enzymes manage to control both, a highly nucleophilic Me+-species and a reactive primary 50 -adenosylradical at the same time. It is Joan Brodericks’ review that provides state-of-the-art insight into the newest results related to the structure and the mechanisms employed by radical SAM enzymes to control the highly reactive intermediates involved in the transformation of canonical bases during posttranslational modification reactions. Finally, we know for many years that such 4Fe/4S-radical SAM enzymes are also key DNA repair enzymes, which repair spore DNA lesions. These DNA lesions form upon reaction of two neighboring dT-residues to a discrete dinucleotide lesion in response to UV light. While socalled CPD and (6-4) lesions are formed upon UV irradia-
Current Opinion in Structural Biology 2012, 22:689–690
tion in normal DNA, it is the unusual structure of the DNA molecules packed in spores that leads to the exclusive formation of a particular lesion in spore DNA. These spore lesions block DNA-based processes, which hinder spores to germinate. The spore photoproduct lyase is able to convert the spore lesion directly back into two dTbases, utilizing a complex radical reaction cascade triggered by the 5-adenosylradical. In the review written by Benjdia the recently solved first crystal structure of a spore photoproduct lyase and the mechanism of the repair enzyme is reviewed. In particular, the structural similarities and differences between the spore photoproduct lyase and other repair enzymes involved in the direct removal of dT-dinucleotide UV lesions [CPD photolyases and (6-4)-photolyases] are discussed. Equally interesting are the PARP enzymes, which install one of the largest posttranslational modification known. In response to DNA damage the enzymes perform an auto-modification and they also modify proteins close by. A double stranded break, for example, triggers the polymerization of NAD+ to give a branched poly-ADPribose polymer attached to critical residues. It is this polymer that forms the posttranslational modification. Andreas Ladurner in his review explains how these enzymes fold to recognize aberrant DNA structures which trigger the interesting auto-modifying polymerization reaction. In summary the four reviews report how special protein structures enable chemistry that goes far beyond of what a chemist can perform in a reaction flask. Controlling the environment around the bound substrates and reagents is the key element to success. The reviewed enzymes have learned to master ‘environmental control’. They create and control precisely the interactions of key protein residues with the substrate and the needed coenzymes and co-substrates. Often even the different parts of the substrate are differently ‘solvated’ in order to control, for example, the direction of critical electron transfer pathways. Establishing defined reaction environments enables chemistry that is impossible in round bottom flask, where the substrate and the reagents enjoy not only the same but also a homogenous surrounding given by the solvent in which the reaction in performed.
www.sciencedirect.com
Catalysis and regulation Editorial overview Thomas Carell Current Opinion in Structural Biology 2012, 22: 689–690 For a complete overview see the Issue Available online 8th November 2012 0959-440X/$ – see front matter, # 2012 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.sbi.2012.10.006
Thomas Carell Department of Chemistry, LudwigMaximilians-Universita¨t (LMU), Butenandtstr. 5-13 (Haus F), Mu¨nchen D-81377, Germany e-mail: [email protected] Thomas Carell is a professor for Organic Chemistry to the Ludwig-MaximiliansUniversita¨t (LMU) in Munich (Germany). The Carell Group is a research group concentrating on nucleic acid chemistry at the Ludwig-Maximilians-Universita¨t Mu¨nchen. Our projects present a wide variety throughout the field including, for example, DNA damage and repair, DNA modifications in epigenetics and click chemistry. To achieve our goals we combine classical organic synthesis with protein biochemistry.
Standard biochemistry textbooks depict in those sections where DNA and RNA are discussed the four Watson Crick bases and they show the 20 standard, canonical, amino acids as the central building block of proteins. We know for a long time that this view is far too simple. All biomolecules including proteins and nucleic acids are often heavily modified posttranslationally and the underlying modification chemistry goes far beyond simple phosphorylations of serine and threonine residues or the ubiquitinylation of proteins needed to tag them for degradation. We understand today that the reversible methylation, acetylation, malonylation, crotonylation or even citrullinylation, to name just a few, of key lysine residues, for example, in histone tails, establish a type of epigenetic genetic code that goes beyond the sequence code. On the DNA level we see that the cytosine residues are either methylated (mC), hydroxymethylated (hmC), formylated (fC) or carboxylated (caC) at position C5 and while we have a good picture of the biological function of mC, the functional role of all the other newly discovered dC-modifications remains to be elucidated. We are learning that radical enzymes are of key importance to manipulate the canonical bases and amino acids in order to establish or erase the modifications discussed above. As such they are essential for establishing a reversible modification chemistry that encodes (epigenetic)-information that we are just beginning to decipher. In the whole field of posttranslational modifications we find the radical SAM enzymes in essential positions. They employ complex chemistry and control highly reactive intermediates in order to allow manipulation of the canonical biomolecules. a-Ketoglutarate-dependent oxidases activate oxygen and they split the oxygen molecule in order to transfer one oxygen atom to the substrate. The other oxygen atom is used to perform the simultaneous oxidative decarboxylation of the co-substrate a-ketoglutarate. Enzymes using this chemistry are responsible for the formation of the mentioned dC-derivative hmC, fC and caC, which are believed to be essential for correct cellular development. In this context a-ketoglutarate oxidizes in TET1-3 the substrate mC in a stepwise fashion to first hmC and then fC and caC. Other a-ketoglutarate enzymes are essential for the demethylation of trimethylated lysine residues in histone tails. Mono-methyllysine and di-methyllysine residues (–NMe1/2) can be quickly oxidized with flavin-dependent oxidases. The key step is a single electron transfer from the amine lone pair to the flavin cofactor bound in the enzyme followed by a loss of a proton to give an imine intermediate. This subsequently hydrolyses in the aqueous environment to give formaldehyde and the demethylated amine. This type of chemistry can, however, not be employed for the demethylation of trimethyllysine residues (–N+Me3), which lack the electron donating N-lone pair. Here aketoglutarate-dependent oxidizations are again needed, which convert one
www.sciencedirect.com
Current Opinion in Structural Biology 2012, 22:689–690
690 Catalysis and regulation
of the methyl groups into a hydroxymethyl moiety thereby creating an N,O-acetal [–N(Me)CH2OH], which hydrolyzes quickly. Christopher Schofield gives in his review an overview about this interesting class of proteins and summarized — based on recent crystal structures — the structural prerequisites that enable the proteins control of the complex radical-based oxidation chemistry. Other radical enzymes that are involved to establish posttranslational modification are 4Fe/4S-cluster containing SAM enzymes, which, for example, transfer methyl groups to RNA bases in order to create methylated noncanonical bases within RNA. Here a reductase first reduces and thereby activates the 4Fe/4S cluster, which subsequently donates an electron to the S-adenosylmethionine cofactor/cosubstrate (SAM) converting it into the highly reactive 5-adenosylradical. This elusive species can either initiate the reaction directly by abstracting an H-atom from the substrate or alternatively, it abstracts an H-atom from a nearby glycine residue creating a glycine radical, which then acts as a resting state for the protein. In these enzymes, it is the glycine radical which initiates catalysis by H-atom transfer from the substrate. Most recently it was discovered that some of the radical-SAM enzymes, involved, for example, in the methylation of adenine residues at position C(3), use two SAM molecules during catalysis. One is needed to start the radical chemistry while the second SAM molecule donates the methylgroup as a Me+-equivalent. These enzymes manage to control both, a highly nucleophilic Me+-species and a reactive primary 50 -adenosylradical at the same time. It is Joan Brodericks’ review that provides state-of-the-art insight into the newest results related to the structure and the mechanisms employed by radical SAM enzymes to control the highly reactive intermediates involved in the transformation of canonical bases during posttranslational modification reactions. Finally, we know for many years that such 4Fe/4S-radical SAM enzymes are also key DNA repair enzymes, which repair spore DNA lesions. These DNA lesions form upon reaction of two neighboring dT-residues to a discrete dinucleotide lesion in response to UV light. While socalled CPD and (6-4) lesions are formed upon UV irradia-
Current Opinion in Structural Biology 2012, 22:689–690
tion in normal DNA, it is the unusual structure of the DNA molecules packed in spores that leads to the exclusive formation of a particular lesion in spore DNA. These spore lesions block DNA-based processes, which hinder spores to germinate. The spore photoproduct lyase is able to convert the spore lesion directly back into two dTbases, utilizing a complex radical reaction cascade triggered by the 5-adenosylradical. In the review written by Benjdia the recently solved first crystal structure of a spore photoproduct lyase and the mechanism of the repair enzyme is reviewed. In particular, the structural similarities and differences between the spore photoproduct lyase and other repair enzymes involved in the direct removal of dT-dinucleotide UV lesions [CPD photolyases and (6-4)-photolyases] are discussed. Equally interesting are the PARP enzymes, which install one of the largest posttranslational modification known. In response to DNA damage the enzymes perform an auto-modification and they also modify proteins close by. A double stranded break, for example, triggers the polymerization of NAD+ to give a branched poly-ADPribose polymer attached to critical residues. It is this polymer that forms the posttranslational modification. Andreas Ladurner in his review explains how these enzymes fold to recognize aberrant DNA structures which trigger the interesting auto-modifying polymerization reaction. In summary the four reviews report how special protein structures enable chemistry that goes far beyond of what a chemist can perform in a reaction flask. Controlling the environment around the bound substrates and reagents is the key element to success. The reviewed enzymes have learned to master ‘environmental control’. They create and control precisely the interactions of key protein residues with the substrate and the needed coenzymes and co-substrates. Often even the different parts of the substrate are differently ‘solvated’ in order to control, for example, the direction of critical electron transfer pathways. Establishing defined reaction environments enables chemistry that is impossible in round bottom flask, where the substrate and the reagents enjoy not only the same but also a homogenous surrounding given by the solvent in which the reaction in performed.
www.sciencedirect.com