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ScienceDirect Editorial overview: Catalysis and regulation: Enzyme catalysis, biosynthetic pathways and regulation James H Naismith and Emily J Parker Current Opinion in Structural Biology 2014, 29:iv–v For a complete overview see the Issue Available online 2nd December 2014 http://dx.doi.org/10.1016/j.sbi.2014.11.004 0959-440X/# 2014 Elsevier Ltd. All rights reserved.
James H Naismith Bishop Wardlaw Professor of Chemical Biology, Royal Society Wolfson Research Merit Award Holder, BSRC, The North Haugh, The University, St Andrews KY16 9ST, UK e-mail: [email protected] Jim Naismith trained as a chemist at Edinburgh becoming a structural biologist during his PhD at Manchester (both UK). After a post-doc with Steve Sprang in Dallas, Texas he started a lab in St Andrews in 1995. He is now Bishop Wardlaw Professor of Chemical Biology. His lab is best known for structures and mechanisms of biosynthetic enzymes, particularly carbohydrate utilizing enzymes with a recent highlight being the first molecular description of a so-called ‘molecular ruler’. Over ten years after mapping out the structural and mechanistic biology of the four enzymes in the dTDP-L-rhamnose pathway, the lab finally reported a nM inhibitor of the first enzyme RmlA. The inhibitor operates by a very unusual mechanism, being entirely competitive in kinetics but binding at an allosteric site. A growing interest has been the structure of membrane proteins from both inner and outer membranes of bacteria, hia lab have recently determined the structure of a novel outer membrane lectin.
Emily J Parker Department of Chemistry, University of Canterbury, Private Bag 4800, Christchurch, New Zealand e-mail: [email protected] Emily Parker completed her BSc(Hons) degree in organic chemistry at the University of Canterbury. She was awarded a commonwealth scholarship to the University of Cambridge, UK, where she completed a PhD in bio-organic chemistry in 1997. After a brief period as a postdoctoral fellow at the University of Cambridge, she returned to New Zealand in 1998 to take up a lectureship at Massey University. In 2006 she moved to the University of Canterbury where she is now the Director of the Biomolecular Interaction Centre and a Professor in the Chemistry Department. Her research team explores the evolution and molecular details of enzymic catalysis and allosteric regulation.
Enzymes accomplish remarkable rate accelerations by reducing the energy barrier of chemical transformations thereby bringing complex chemistry into biological timescales making life possible. The regulation of enzymatic catalytic efficiency is an important feature of metabolic sophistication and allows organisms to respond to supply and demand constrains. Structural biology plays a central role in understanding enzyme function and since evolution conserves structure not sequence, structural biology often serves to highlight the common chemical step in apparently disparate enzymes. Ultra high resolution X-ray crystallography, by locating atoms including hydrogens with extraordinary precision, is changing and deepening our knowledge of catalysis. Tittman and Neumann outline the challenges of and the experimental approaches needed to obtain such ultra high resolution data. They demonstrate how such data have transformed the understanding of several enzymatic reaction mechanisms; by disclosing hitherto unsuspected bond distortions, protonation states and in one case the correcting the chemical structure of cofactor. These are not minor details, chemistry at its core is the making and breaking of bonds, seeing molecules distort as they approach their transition state allows chemistry to be observed. Acid–base chemistry in enzyme catalysis is invoked often based on reasoning, experimentally identifying the location of protons not only resolves ambiguities but also has changed assumptions. At the more common lower resolutions, structural biology is turning genomic data into biochemical insight. The production of phenazines reviewed by Blankenfeldt and Parsons and thiamine by Fitzpatrick and Thore are perfect examples how biology accomplishes complex transformations that inspire organic chemists and create powerful molecules. Thiamine has been known to be a key molecule in metabolism for over 100 years, yet the full details of biosynthesis of this important vitamin are only now being revealed. One of the most remarkable findings is the role of two ‘suicide enzymes’ in this pathway. These proteins essentially act as co-substrates and are thus single-turnover enzymes. One enzyme delivers sulfur from cysteine and other the imidazole from histidine, with these functional groups going on to be incorporated into the thiazole and pyrimidine precursors respectively. Fitzpatrick and Thore also consider recent studies describing the regulation of thiamine biosynthesis by riboswitches and its degradation by thiaminases. Phenazines are colored nitrogen containing aromatic compounds that have now been shown to possess activity as antibiotics, virulence factors and as well as respiratory pigments. As with thiamine, phenazines (due to their color) have been known about for years, but only very recently have the key biosynthetic steps been delineated.
Current Opinion in Structural Biology 2014, 29:iv–v
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Editorial overview Naismith and Parker 5
The biosynthetic pathways of two ribosomally synthesized peptide natural products, the lanthobiotics (van der Donk and Nair) and patellamides (Koehnke et al.) contain multiple enzymes catalyzing different transformations. Lanthipeptides are post-translationally modified peptide natural products containing thioether cross link and lantibiotics are a subgroup of the lanthipeptides that show antibacterial action. Van der Donk and Nair focus on nisin, which disrupts the integrity of the cell wall of Grampositive bacteria. Two key enzymes catalyze the formation of the thioether bonds: a dehydratase and a cyclase. Recent biochemical evidence suggests the dehydratase catalyses the glutamylation and elimination steps to give dehydroalaninyl or dehydrobutyrinyl residues, via action at two distinct active sites. Koehnke et al. review the current understanding biosynthesis of patellamide, a process involving seven different chemistries. Structures remain the most powerful tool in identifying evolutionary connections between proteins and these studies have revealed new relationships within and between the enzymes in these and other pathways. In both cases, the studies are underpinning the rational manipulation of these pathways to produce novel biomolecules for the treatment of diseases and for use as biotechnological tools. The regulation of enzymatic catalysis by allostery plays an important role in the control of many biosynthetic pathways. The so-called ACT domain is a small and highly divergent protein domain that regulates many metabolic enzymes in an allosteric manner. Its divergence has made its identification from sequence alone problematic. Lang et al. review the function of the ACT domain in controlling enzymes in the biosynthesis of amino acids and
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propose a combined sequence/structure/function approach to aid in its identification. The transfer of the ACT domain to an unregulated enzyme can confer allosteric regulation, providing insights into the evolution of allostery and the gene fusion events that have led to its acquisition. Proteins dynamics and associated conformational changes are a feature of the regulation of membrane trafficking. Archbold et al. review the structural features and the role of the Sec1/Munc18 (SM) proteins and their role in interacting with syntaxin to promote membrane fusion. Syntaxin is thought to undergo conformational transition from a closed to an open form to enable it to react with is fusion partners and the SM proteins may play an important regulatory role in this process. Conformational differences in the SM proteins are also now well documented and Archbold et al. speculate that N-peptide binding of syntaxin is required to enable conformational change. This idea would provide a clear functional demarcation between the two classes of SM proteins, those that either use the N-peptide binding mode or do not. Enzymes are nature’s verbs, the doing things. A common refrain is that structural biology has moved beyond the study of enzymes, that cutting edge work focuses on protein–protein complexes in human systems. Whilst the insights gained from such studies are indeed transforming biology and medicine, as this collection of reviews shows, there are just as important and transformational insights to be gained from enzymes. What is clear is that in every case, structural biology is but one part of the arsenal, yet the clarity it provides to thinking about mechanism ensures it remains both relevant and critical.
Current Opinion in Structural Biology 2014, 29:iv–v
ScienceDirect Editorial overview: Catalysis and regulation: Enzyme catalysis, biosynthetic pathways and regulation James H Naismith and Emily J Parker Current Opinion in Structural Biology 2014, 29:iv–v For a complete overview see the Issue Available online 2nd December 2014 http://dx.doi.org/10.1016/j.sbi.2014.11.004 0959-440X/# 2014 Elsevier Ltd. All rights reserved.
James H Naismith Bishop Wardlaw Professor of Chemical Biology, Royal Society Wolfson Research Merit Award Holder, BSRC, The North Haugh, The University, St Andrews KY16 9ST, UK e-mail: [email protected] Jim Naismith trained as a chemist at Edinburgh becoming a structural biologist during his PhD at Manchester (both UK). After a post-doc with Steve Sprang in Dallas, Texas he started a lab in St Andrews in 1995. He is now Bishop Wardlaw Professor of Chemical Biology. His lab is best known for structures and mechanisms of biosynthetic enzymes, particularly carbohydrate utilizing enzymes with a recent highlight being the first molecular description of a so-called ‘molecular ruler’. Over ten years after mapping out the structural and mechanistic biology of the four enzymes in the dTDP-L-rhamnose pathway, the lab finally reported a nM inhibitor of the first enzyme RmlA. The inhibitor operates by a very unusual mechanism, being entirely competitive in kinetics but binding at an allosteric site. A growing interest has been the structure of membrane proteins from both inner and outer membranes of bacteria, hia lab have recently determined the structure of a novel outer membrane lectin.
Emily J Parker Department of Chemistry, University of Canterbury, Private Bag 4800, Christchurch, New Zealand e-mail: [email protected] Emily Parker completed her BSc(Hons) degree in organic chemistry at the University of Canterbury. She was awarded a commonwealth scholarship to the University of Cambridge, UK, where she completed a PhD in bio-organic chemistry in 1997. After a brief period as a postdoctoral fellow at the University of Cambridge, she returned to New Zealand in 1998 to take up a lectureship at Massey University. In 2006 she moved to the University of Canterbury where she is now the Director of the Biomolecular Interaction Centre and a Professor in the Chemistry Department. Her research team explores the evolution and molecular details of enzymic catalysis and allosteric regulation.
Enzymes accomplish remarkable rate accelerations by reducing the energy barrier of chemical transformations thereby bringing complex chemistry into biological timescales making life possible. The regulation of enzymatic catalytic efficiency is an important feature of metabolic sophistication and allows organisms to respond to supply and demand constrains. Structural biology plays a central role in understanding enzyme function and since evolution conserves structure not sequence, structural biology often serves to highlight the common chemical step in apparently disparate enzymes. Ultra high resolution X-ray crystallography, by locating atoms including hydrogens with extraordinary precision, is changing and deepening our knowledge of catalysis. Tittman and Neumann outline the challenges of and the experimental approaches needed to obtain such ultra high resolution data. They demonstrate how such data have transformed the understanding of several enzymatic reaction mechanisms; by disclosing hitherto unsuspected bond distortions, protonation states and in one case the correcting the chemical structure of cofactor. These are not minor details, chemistry at its core is the making and breaking of bonds, seeing molecules distort as they approach their transition state allows chemistry to be observed. Acid–base chemistry in enzyme catalysis is invoked often based on reasoning, experimentally identifying the location of protons not only resolves ambiguities but also has changed assumptions. At the more common lower resolutions, structural biology is turning genomic data into biochemical insight. The production of phenazines reviewed by Blankenfeldt and Parsons and thiamine by Fitzpatrick and Thore are perfect examples how biology accomplishes complex transformations that inspire organic chemists and create powerful molecules. Thiamine has been known to be a key molecule in metabolism for over 100 years, yet the full details of biosynthesis of this important vitamin are only now being revealed. One of the most remarkable findings is the role of two ‘suicide enzymes’ in this pathway. These proteins essentially act as co-substrates and are thus single-turnover enzymes. One enzyme delivers sulfur from cysteine and other the imidazole from histidine, with these functional groups going on to be incorporated into the thiazole and pyrimidine precursors respectively. Fitzpatrick and Thore also consider recent studies describing the regulation of thiamine biosynthesis by riboswitches and its degradation by thiaminases. Phenazines are colored nitrogen containing aromatic compounds that have now been shown to possess activity as antibiotics, virulence factors and as well as respiratory pigments. As with thiamine, phenazines (due to their color) have been known about for years, but only very recently have the key biosynthetic steps been delineated.
Current Opinion in Structural Biology 2014, 29:iv–v
www.sciencedirect.com
Editorial overview Naismith and Parker 5
The biosynthetic pathways of two ribosomally synthesized peptide natural products, the lanthobiotics (van der Donk and Nair) and patellamides (Koehnke et al.) contain multiple enzymes catalyzing different transformations. Lanthipeptides are post-translationally modified peptide natural products containing thioether cross link and lantibiotics are a subgroup of the lanthipeptides that show antibacterial action. Van der Donk and Nair focus on nisin, which disrupts the integrity of the cell wall of Grampositive bacteria. Two key enzymes catalyze the formation of the thioether bonds: a dehydratase and a cyclase. Recent biochemical evidence suggests the dehydratase catalyses the glutamylation and elimination steps to give dehydroalaninyl or dehydrobutyrinyl residues, via action at two distinct active sites. Koehnke et al. review the current understanding biosynthesis of patellamide, a process involving seven different chemistries. Structures remain the most powerful tool in identifying evolutionary connections between proteins and these studies have revealed new relationships within and between the enzymes in these and other pathways. In both cases, the studies are underpinning the rational manipulation of these pathways to produce novel biomolecules for the treatment of diseases and for use as biotechnological tools. The regulation of enzymatic catalysis by allostery plays an important role in the control of many biosynthetic pathways. The so-called ACT domain is a small and highly divergent protein domain that regulates many metabolic enzymes in an allosteric manner. Its divergence has made its identification from sequence alone problematic. Lang et al. review the function of the ACT domain in controlling enzymes in the biosynthesis of amino acids and
www.sciencedirect.com
propose a combined sequence/structure/function approach to aid in its identification. The transfer of the ACT domain to an unregulated enzyme can confer allosteric regulation, providing insights into the evolution of allostery and the gene fusion events that have led to its acquisition. Proteins dynamics and associated conformational changes are a feature of the regulation of membrane trafficking. Archbold et al. review the structural features and the role of the Sec1/Munc18 (SM) proteins and their role in interacting with syntaxin to promote membrane fusion. Syntaxin is thought to undergo conformational transition from a closed to an open form to enable it to react with is fusion partners and the SM proteins may play an important regulatory role in this process. Conformational differences in the SM proteins are also now well documented and Archbold et al. speculate that N-peptide binding of syntaxin is required to enable conformational change. This idea would provide a clear functional demarcation between the two classes of SM proteins, those that either use the N-peptide binding mode or do not. Enzymes are nature’s verbs, the doing things. A common refrain is that structural biology has moved beyond the study of enzymes, that cutting edge work focuses on protein–protein complexes in human systems. Whilst the insights gained from such studies are indeed transforming biology and medicine, as this collection of reviews shows, there are just as important and transformational insights to be gained from enzymes. What is clear is that in every case, structural biology is but one part of the arsenal, yet the clarity it provides to thinking about mechanism ensures it remains both relevant and critical.
Current Opinion in Structural Biology 2014, 29:iv–v
