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Editorial overview: Catalysis and regulation
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ScienceDirect Editorial overview: Catalysis and regulation Judith P Klinman and Amy C Rosenzweig Current Opinion in Structural Biology 2015, 35:iv–vi For a complete overview see the Issue Available online 10th November 2015 http://dx.doi.org/10.1016/j.sbi.2015.10.003 0959-440X/# 2015 Elsevier Ltd. All rights reserved.
Judith P Klinman1,2,3 1
Department of Chemistry, University of California, Berkeley, CA, USA 2
Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA 3 California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California, USA e-mail: [email protected]
Judith Klinman received her A.B. and Ph.D. degrees at the University of Pennsylvania. After a year of postdoctoral research at the Weizmann Institute, Rehovot, Israel, she moved to the Institute for Cancer Research, Fox Chase, Philadelphia. After several years of postdoctoral study with Irwin Rose at ICR, she advanced to an independent research position, remaining there until 1978. In that year she joined the faculty of the University of California, Berkeley, where she is now Professor Emerita of Chemistry and of Molecular and Cell Biology. Her research is focused on quantum effects (tunneling) in enzyme catalysis and their relationship to the role of protein dynamics in achieving very high catalytic rate accelerations. Other areas of active research include enzymatic methyl transfer reactions, the nature of molecular oxygen activation in biological systems, and the biosynthesis and function of the family of quino-cofactors that include TPQ, LTQ, TTQ, CTQ and PQQ.
Amy C Rosenzweig1,2 1 Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA 2
Department of Chemistry, Northwestern University, Evanston, IL, USA e-mail: [email protected]
Amy Rosenzweig received a B.A. in chemistry from Amherst College where she became interested in bioinorganic chemistry in David Dooley’s laboratory. She went on to obtain a Ph.D. in inorganic chemistry from Massachusetts Institute of Technology working with Stephen Lippard. After an NIH postdoctoral fellowship in structural biology
Although the pursuit of protein structure and function has occupied a central niche in the fields of biophysics and biochemistry for decades, our understanding of protein catalysis and regulation remains incomplete. Despite the exponential growth in the number of protein structures deposited in the PDB (>112,000 to date) many challenges still exist, including the ability to obtain unambiguous atomic detail from ultra-high resolution structures and the monitoring of protein dynamics in a spatially resolved manner. In addition, structural characterization of complex multidomain proteins, particularly those that undergo functionally important conformational changes, remains difficult. In this issue of COSTBI 2015, Burger et al. address challenges and benefits associated with ultra-high resolution crystal structures with an emphasis on metalloenzyme active sites. One common problem is that metal centers can be photoreduced by X-rays, leading to a non-physiological or altered state. Assignment of individual metal ion redox states in a crystal structure can be accomplished by the powerful protocol of spatially refined anomalous dispersion analysis. Another potential issue is accurate assignment of atom identity, which can be achieved for metal ions through careful collection of anomalous diffraction data and for light atoms via electron density analysis if a resolution of 1.0 A˚ or better is obtained. Notably, this approach resolved the nature of the central carbon atom in the nitrogenase MoFe cofactor. Also challenging is the detection of hydrogen atoms and the possible presence of hydride. Finally, the authors provide a cautionary tale about Fourier series termination artifacts, with illustrative examples involving tungsten and iron sites. Advances in high resolution structure analysis are complemented by recent work summarized by Levantino et al. aimed at spatial resolution of protein motions over a wide range of time scales. In the absence of suitable crystals, changes in protein shape can be discerned using X-ray scattering methods such as SAXS and WAXS in combination with rapid mixing techniques. X-ray diffraction methods can provide higher resolution dynamical information. Importantly, the development of X-ray free electron lasers has opened up the potential to extend dynamical measurements to the very fast, subpicosecond time frame. In all instances, the question of how to initiate a reaction is crucial, with light activation the current method of choice. Photoactivated proteins are the most amenable to immediate characterization, with other studies awaiting the application of suitable photo-labile protecting groups for either proteins or substrates. The authors also mention the possible use of temperature jump on preformed protein/small ligand complexes. This review shows that while time dependent X-ray approaches remain in their infancy, the field is at an exciting juncture.
Current Opinion in Structural Biology 2015, 35:iv–vi
www.sciencedirect.com
Editorial overview Klinman and Rosenzweig
at Harvard Medical School, she joined the faculty of Northwestern in 1997. She is currently the Weinberg Family Distinguished Professor of Life Sciences in the Departments of Molecular Biosciences and of Chemistry. Her research interests include biological methane oxidation, metal uptake and transport, oxygen activation by metalloenzymes, and membrane metalloproteins.
v
Many systems that could benefit from time resolved studies of conformational changes involve multidomain proteins. Anders and Essen focus on a multidomain photoreceptors with potential uses as biomarkers and biosensors or in light-regulated gene expression. GAF domain photoreceptors that use bilins as a chromophore can be divided into groups on the basis of their domain architecture; the groups are structurally related, but exhibit some key differences. Crystallographic and electron microscopy studies have revealed structural changes that occur upon photoconversion and provide key insight into how these changes may effect downstream signaling. Such information is integral to current efforts directed at engineering these photoreceptors for practical applications. Domain–domain interactions and conformational changes are also important in enzymes, including the aromatic amino acid hydroxylases reviewed by Fitzpatrick. The interaction of regulatory and catalytic domains in this important class of neurotransmitter producing enzymes, which includes phenylalanine, tyrosine and tryptophan hydroxylases, has been hampered by the lack of full length protein structures containing both domains. Combining the available structural data, Fitzpatrick presents plausible models for the regulation of both phenylalanine and tyrosine hydroxylases. Interestingly, the mode of regulation appears to be quite different with substrate activation at an allosteric site in the case of phenylalanine hydroxylase and product inhibition at the active site of tyrosine hydroxylase. If full length structures can be obtained in the future, it will be fascinating to see whether they are compatible with the models derived from individual protein domains. Fujimori builds on the theme of interacting domains, reviewing histone modification via reversible methylation/demethylation processes. The involved enzymes and domains are referred to as ‘writers’ (methyl transferases), ‘erasers’ (demethylases), and ‘readers’ (regulatory domains). Fujimori describes how readers can act either as cis-regulatory or transregulatory elements. A recent fascinating finding shows how the regulatory N-terminal domain of a yeast lysine methyl transferase (H3K9) recognizes the trimethylated lysine product, activating the enzyme’s catalytic domain for further methylation at an unmodified histone on a neighboring nucleosome. Finally, two reviews address exciting and timely aspects of enzyme catalysis. Span and Marletta summarize the structural knowledge regarding the emergent family of copper-containing polysaccharide modifying monooxygenases (PMOs). These enzymes cleave glycosidic bonds, and have received much attention for their potential applications in biomass conversion. The enzymes feature a conserved b-sandwich fold with a flat, shallow substrate binding site, and a mononuclear copper active center. Intriguingly, PMO homologs have now been implicated in bacterial and viral pathogenesis. Characterization of these newly identified family members will probably reveal structural variations and provide insight into how PMOs perform divergent functions. Bandarian and Drennan focus on the radical SAM chemistry employed by microorganisms in the post-translational modification pathways that produce deazapurines. Compounds within this class show promise as possible herbicidal, antibacterial, antifungal or antineoplastic agents. Careful detective work led to the identification of operons encoding the deazapurine biosynthetic enzymes. The first step in this biosynthetic pathway is catalyzed by 7-carboxy7-deazaguanine (CDG) synthase, a radical SAM enzyme that generates its
www.sciencedirect.com
Current Opinion in Structural Biology 2015, 35:iv–vi
vi Catalysis and regulations
active site using a non-canonical CX14CX2C iron sulfur center. A creative combination of biochemical and structural studies on CDG synthase has produced a detailed reaction mechanism for this complex, radical based, ring contraction process. These reviews, although focused on a range of topics, underscore the interplay between structural biology, biophysics, and biochemistry as well as the potential for advanced structural techniques, both static and dynamic, to elucidate new mechanisms of catalysis and regulation.
Current Opinion in Structural Biology 2015, 35:iv–vi
Combining ultra-high resolution X-ray analysis with emerging time resolved techniques will no doubt lead to major discoveries. Recent progress toward understanding the molecular details of photoreceptor function, allosteric regulation of aromatic amino acid hydroxylases, histone and DNA methylation, and catalysis by PMOs and CDG synthase are just a few examples of how structural biology impacts diverse fields. This type of in depth interrogation of structure and mechanism remains the bullwark for future advances in technology and biomedicine.
www.sciencedirect.com
ScienceDirect Editorial overview: Catalysis and regulation Judith P Klinman and Amy C Rosenzweig Current Opinion in Structural Biology 2015, 35:iv–vi For a complete overview see the Issue Available online 10th November 2015 http://dx.doi.org/10.1016/j.sbi.2015.10.003 0959-440X/# 2015 Elsevier Ltd. All rights reserved.
Judith P Klinman1,2,3 1
Department of Chemistry, University of California, Berkeley, CA, USA 2
Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA 3 California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California, USA e-mail: [email protected]
Judith Klinman received her A.B. and Ph.D. degrees at the University of Pennsylvania. After a year of postdoctoral research at the Weizmann Institute, Rehovot, Israel, she moved to the Institute for Cancer Research, Fox Chase, Philadelphia. After several years of postdoctoral study with Irwin Rose at ICR, she advanced to an independent research position, remaining there until 1978. In that year she joined the faculty of the University of California, Berkeley, where she is now Professor Emerita of Chemistry and of Molecular and Cell Biology. Her research is focused on quantum effects (tunneling) in enzyme catalysis and their relationship to the role of protein dynamics in achieving very high catalytic rate accelerations. Other areas of active research include enzymatic methyl transfer reactions, the nature of molecular oxygen activation in biological systems, and the biosynthesis and function of the family of quino-cofactors that include TPQ, LTQ, TTQ, CTQ and PQQ.
Amy C Rosenzweig1,2 1 Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA 2
Department of Chemistry, Northwestern University, Evanston, IL, USA e-mail: [email protected]
Amy Rosenzweig received a B.A. in chemistry from Amherst College where she became interested in bioinorganic chemistry in David Dooley’s laboratory. She went on to obtain a Ph.D. in inorganic chemistry from Massachusetts Institute of Technology working with Stephen Lippard. After an NIH postdoctoral fellowship in structural biology
Although the pursuit of protein structure and function has occupied a central niche in the fields of biophysics and biochemistry for decades, our understanding of protein catalysis and regulation remains incomplete. Despite the exponential growth in the number of protein structures deposited in the PDB (>112,000 to date) many challenges still exist, including the ability to obtain unambiguous atomic detail from ultra-high resolution structures and the monitoring of protein dynamics in a spatially resolved manner. In addition, structural characterization of complex multidomain proteins, particularly those that undergo functionally important conformational changes, remains difficult. In this issue of COSTBI 2015, Burger et al. address challenges and benefits associated with ultra-high resolution crystal structures with an emphasis on metalloenzyme active sites. One common problem is that metal centers can be photoreduced by X-rays, leading to a non-physiological or altered state. Assignment of individual metal ion redox states in a crystal structure can be accomplished by the powerful protocol of spatially refined anomalous dispersion analysis. Another potential issue is accurate assignment of atom identity, which can be achieved for metal ions through careful collection of anomalous diffraction data and for light atoms via electron density analysis if a resolution of 1.0 A˚ or better is obtained. Notably, this approach resolved the nature of the central carbon atom in the nitrogenase MoFe cofactor. Also challenging is the detection of hydrogen atoms and the possible presence of hydride. Finally, the authors provide a cautionary tale about Fourier series termination artifacts, with illustrative examples involving tungsten and iron sites. Advances in high resolution structure analysis are complemented by recent work summarized by Levantino et al. aimed at spatial resolution of protein motions over a wide range of time scales. In the absence of suitable crystals, changes in protein shape can be discerned using X-ray scattering methods such as SAXS and WAXS in combination with rapid mixing techniques. X-ray diffraction methods can provide higher resolution dynamical information. Importantly, the development of X-ray free electron lasers has opened up the potential to extend dynamical measurements to the very fast, subpicosecond time frame. In all instances, the question of how to initiate a reaction is crucial, with light activation the current method of choice. Photoactivated proteins are the most amenable to immediate characterization, with other studies awaiting the application of suitable photo-labile protecting groups for either proteins or substrates. The authors also mention the possible use of temperature jump on preformed protein/small ligand complexes. This review shows that while time dependent X-ray approaches remain in their infancy, the field is at an exciting juncture.
Current Opinion in Structural Biology 2015, 35:iv–vi
www.sciencedirect.com
Editorial overview Klinman and Rosenzweig
at Harvard Medical School, she joined the faculty of Northwestern in 1997. She is currently the Weinberg Family Distinguished Professor of Life Sciences in the Departments of Molecular Biosciences and of Chemistry. Her research interests include biological methane oxidation, metal uptake and transport, oxygen activation by metalloenzymes, and membrane metalloproteins.
v
Many systems that could benefit from time resolved studies of conformational changes involve multidomain proteins. Anders and Essen focus on a multidomain photoreceptors with potential uses as biomarkers and biosensors or in light-regulated gene expression. GAF domain photoreceptors that use bilins as a chromophore can be divided into groups on the basis of their domain architecture; the groups are structurally related, but exhibit some key differences. Crystallographic and electron microscopy studies have revealed structural changes that occur upon photoconversion and provide key insight into how these changes may effect downstream signaling. Such information is integral to current efforts directed at engineering these photoreceptors for practical applications. Domain–domain interactions and conformational changes are also important in enzymes, including the aromatic amino acid hydroxylases reviewed by Fitzpatrick. The interaction of regulatory and catalytic domains in this important class of neurotransmitter producing enzymes, which includes phenylalanine, tyrosine and tryptophan hydroxylases, has been hampered by the lack of full length protein structures containing both domains. Combining the available structural data, Fitzpatrick presents plausible models for the regulation of both phenylalanine and tyrosine hydroxylases. Interestingly, the mode of regulation appears to be quite different with substrate activation at an allosteric site in the case of phenylalanine hydroxylase and product inhibition at the active site of tyrosine hydroxylase. If full length structures can be obtained in the future, it will be fascinating to see whether they are compatible with the models derived from individual protein domains. Fujimori builds on the theme of interacting domains, reviewing histone modification via reversible methylation/demethylation processes. The involved enzymes and domains are referred to as ‘writers’ (methyl transferases), ‘erasers’ (demethylases), and ‘readers’ (regulatory domains). Fujimori describes how readers can act either as cis-regulatory or transregulatory elements. A recent fascinating finding shows how the regulatory N-terminal domain of a yeast lysine methyl transferase (H3K9) recognizes the trimethylated lysine product, activating the enzyme’s catalytic domain for further methylation at an unmodified histone on a neighboring nucleosome. Finally, two reviews address exciting and timely aspects of enzyme catalysis. Span and Marletta summarize the structural knowledge regarding the emergent family of copper-containing polysaccharide modifying monooxygenases (PMOs). These enzymes cleave glycosidic bonds, and have received much attention for their potential applications in biomass conversion. The enzymes feature a conserved b-sandwich fold with a flat, shallow substrate binding site, and a mononuclear copper active center. Intriguingly, PMO homologs have now been implicated in bacterial and viral pathogenesis. Characterization of these newly identified family members will probably reveal structural variations and provide insight into how PMOs perform divergent functions. Bandarian and Drennan focus on the radical SAM chemistry employed by microorganisms in the post-translational modification pathways that produce deazapurines. Compounds within this class show promise as possible herbicidal, antibacterial, antifungal or antineoplastic agents. Careful detective work led to the identification of operons encoding the deazapurine biosynthetic enzymes. The first step in this biosynthetic pathway is catalyzed by 7-carboxy7-deazaguanine (CDG) synthase, a radical SAM enzyme that generates its
www.sciencedirect.com
Current Opinion in Structural Biology 2015, 35:iv–vi
vi Catalysis and regulations
active site using a non-canonical CX14CX2C iron sulfur center. A creative combination of biochemical and structural studies on CDG synthase has produced a detailed reaction mechanism for this complex, radical based, ring contraction process. These reviews, although focused on a range of topics, underscore the interplay between structural biology, biophysics, and biochemistry as well as the potential for advanced structural techniques, both static and dynamic, to elucidate new mechanisms of catalysis and regulation.
Current Opinion in Structural Biology 2015, 35:iv–vi
Combining ultra-high resolution X-ray analysis with emerging time resolved techniques will no doubt lead to major discoveries. Recent progress toward understanding the molecular details of photoreceptor function, allosteric regulation of aromatic amino acid hydroxylases, histone and DNA methylation, and catalysis by PMOs and CDG synthase are just a few examples of how structural biology impacts diverse fields. This type of in depth interrogation of structure and mechanism remains the bullwark for future advances in technology and biomedicine.
www.sciencedirect.com