1
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Ghadirian N, Morgan RD, Horton NC. DNA Sequence Control of Enzyme Filamentation and Activation of the SgrAI Endonuclease. Biochemistry 2024; 63:326-338. [PMID: 38207281 DOI: 10.1021/acs.biochem.3c00313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Enzyme polymerization (also known as filamentation) has emerged as a new layer of enzyme regulation. SgrAI is a sequence-dependent DNA endonuclease that forms polymeric filaments with enhanced DNA cleavage activity as well as altered DNA sequence specificity. To better understand this unusual regulatory mechanism, full global kinetic modeling of the reaction pathway, including the enzyme filamentation steps, has been undertaken. Prior work with the primary DNA recognition sequence cleaved by SgrAI has shown how the kinetic rate constants of each reaction step are tuned to maximize activation and DNA cleavage while minimizing the extent of DNA cleavage to the host genome. In the current work, we expand on our prior study by now including DNA cleavage of a secondary recognition sequence, to understand how the sequence of the bound DNA modulates filamentation and activation of SgrAI. The work shows that an allosteric equilibrium between low and high activity states is modulated by the sequence of bound DNA, with primary sequences more prone to activation and filament formation, while SgrAI bound to secondary recognition sequences favor the low (and nonfilamenting) state by up to 40-fold. In addition, the degree of methylation of secondary sequences in the host organism, Streptomyces griseus, is now reported for the first time and shows that as predicted, these sequences are left unprotected from the SgrAI endonuclease making sequence specificity critical in this unusual filament-forming enzyme.
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Affiliation(s)
- Niloofar Ghadirian
- Department of Chemistry & Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
| | - Richard D Morgan
- New England Biolabs, Inc., Ipswich, Massachusetts 01938, United States
| | - Nancy C Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721, United States
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2
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The role of filamentation in activation and DNA sequence specificity of the sequence-specific endonuclease SgrAI. Biochem Soc Trans 2022; 50:1703-1714. [PMID: 36398769 PMCID: PMC9788392 DOI: 10.1042/bst20220547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 10/09/2022] [Accepted: 10/12/2022] [Indexed: 11/19/2022]
Abstract
Filament formation by metabolic, biosynthetic, and other enzymes has recently come into focus as a mechanism to fine-tune enzyme activity in the cell. Filamentation is key to the function of SgrAI, a sequence-specific DNA endonuclease that has served as a model system to provide some of the deepest insights into the biophysical characteristics of filamentation and its functional consequences. Structure-function analyses reveal that, in the filamentous state, SgrAI stabilizes an activated enzyme conformation that leads to accelerated DNA cleavage activity and expanded DNA sequence specificity. The latter is thought to be mediated by sequence-specific DNA structure, protein-DNA interactions, and a disorder-to-order transition in the protein, which collectively affect the relative stabilities of the inactive, non-filamentous conformation and the active, filamentous conformation of SgrAI bound to DNA. Full global kinetic modeling of the DNA cleavage pathway reveals a slow, rate-limiting, second-order association rate constant for filament assembly, and simulations of in vivo activity predict that filamentation is superior to non-filamenting mechanisms in ensuring rapid activation and sequestration of SgrAI's DNA cleavage activity on phage DNA and away from the host chromosome. In vivo studies demonstrate the critical requirement for accelerated DNA cleavage by SgrAI in its biological role to safeguard the bacterial host. Collectively, these data have advanced our understanding of how filamentation can regulate enzyme structure and function, while the experimental strategies used for SgrAI can be applied to other enzymatic systems to identify novel functional roles for filamentation.
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3
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Shan Z, Ghadirian N, Lyumkis D, Horton NC. Pre-Transition State and Apo Structures of the Filament-Forming Enzyme SgrAI Elucidate Mechanisms of Activation and Substrate Specificity. J Biol Chem 2022; 298:101760. [PMID: 35202658 PMCID: PMC8960973 DOI: 10.1016/j.jbc.2022.101760] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 12/01/2022] Open
Abstract
Enzyme filamentation is a widespread phenomenon that mediates enzyme regulation and function. For the filament-forming sequence-specific DNA endonuclease SgrAI, the process of filamentation both accelerates its DNA cleavage activity and expands its DNA sequence specificity, thus allowing for many additional DNA sequences to be rapidly cleaved. Both outcomes—the acceleration of DNA cleavage and the expansion of sequence specificity—are proposed to regulate critical processes in bacterial innate immunity. However, the mechanistic bases underlying these events remain unclear. Herein, we describe two new structures of the SgrAI enzyme that shed light on its catalytic function. First, we present the cryo-EM structure of filamentous SgrAI bound to intact primary site DNA and Ca2+ resolved to ∼2.5 Å within the catalytic center, which represents the trapped enzyme–DNA complex prior to the DNA cleavage reaction. This structure reveals important conformational changes that contribute to the catalytic mechanism and the binding of a second divalent cation in the enzyme active site, which is expected to contribute to increased DNA cleavage activity of SgrAI in the filamentous state. Second, we present an X-ray crystal structure of DNA-free (apo) SgrAI resolved to 2.0 Å resolution, which reveals a disordered loop involved in DNA recognition. Collectively, these multiple new observations clarify the mechanism of expansion of DNA sequence specificity of SgrAI, including the indirect readout of sequence-dependent DNA structure, changes in protein–DNA interactions, and the disorder-to-order transition of a crucial DNA recognition element.
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Affiliation(s)
- Zelin Shan
- Laboratory of Genetics, The Salk Institute of Biological Sciences, La Jolla, CA, USA 92037
| | - Niloofar Ghadirian
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA 85721
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute of Biological Sciences, La Jolla, CA, USA 92037; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA 92037.
| | - N C Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA 85721.
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4
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Park CK, Horton NC. Structures, functions, and mechanisms of filament forming enzymes: a renaissance of enzyme filamentation. Biophys Rev 2019; 11:927-994. [PMID: 31734826 PMCID: PMC6874960 DOI: 10.1007/s12551-019-00602-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Accepted: 10/24/2019] [Indexed: 12/19/2022] Open
Abstract
Filament formation by non-cytoskeletal enzymes has been known for decades, yet only relatively recently has its wide-spread role in enzyme regulation and biology come to be appreciated. This comprehensive review summarizes what is known for each enzyme confirmed to form filamentous structures in vitro, and for the many that are known only to form large self-assemblies within cells. For some enzymes, studies describing both the in vitro filamentous structures and cellular self-assembly formation are also known and described. Special attention is paid to the detailed structures of each type of enzyme filament, as well as the roles the structures play in enzyme regulation and in biology. Where it is known or hypothesized, the advantages conferred by enzyme filamentation are reviewed. Finally, the similarities, differences, and comparison to the SgrAI endonuclease system are also highlighted.
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Affiliation(s)
- Chad K. Park
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721 USA
| | - Nancy C. Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721 USA
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5
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Polley S, Lyumkis D, Horton NC. Mechanism of Filamentation-Induced Allosteric Activation of the SgrAI Endonuclease. Structure 2019; 27:1497-1507.e3. [PMID: 31447289 DOI: 10.1016/j.str.2019.08.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/10/2019] [Accepted: 08/02/2019] [Indexed: 02/07/2023]
Abstract
Filament formation by enzymes is increasingly recognized as an important phenomenon with potentially unique regulatory properties and biological roles. SgrAI is an allosterically regulated type II restriction endonuclease that forms filaments with enhanced DNA cleavage activity and altered sequence specificity. Here, we present the cryoelectron microscopy (cryo-EM) structure of the filament of SgrAI in its activated configuration. The structural data illuminate the mechanistic origin of hyperaccelerated DNA cleavage activity and suggests how indirect DNA sequence readout within filamentous SgrAI may enable recognition of substantially more nucleotide sequences than its low-activity form, thereby altering and partially relaxing its DNA sequence specificity. Together, substrate DNA binding, indirect readout, and filamentation simultaneously enhance SgrAI's catalytic activity and modulate substrate preference. This unusual enzyme mechanism may have evolved to perform the specialized functions of bacterial innate immunity in rapid defense against invading phage DNA without causing damage to the host DNA.
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Affiliation(s)
- Smarajit Polley
- Department of Biophysics, Bose Institute, Kolkata 700054, India
| | - Dmitry Lyumkis
- Laboratory of Genetics, Salk Institute for Biological Studies, La Jolla, CA 92037, USA.
| | - Nancy C Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ 85721, USA.
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Barahona CJ, Basantes LE, Tompkins KJ, Heitman DM, Chukwu BI, Sanchez J, Sanchez JL, Ghadirian N, Park CK, Horton NC. The Need for Speed: Run-On Oligomer Filament Formation Provides Maximum Speed with Maximum Sequestration of Activity. J Virol 2019; 93:e01647-18. [PMID: 30518649 PMCID: PMC6384071 DOI: 10.1128/jvi.01647-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 11/26/2018] [Indexed: 01/29/2023] Open
Abstract
Here, we investigate an unusual antiviral mechanism developed in the bacterium Streptomyces griseus SgrAI is a type II restriction endonuclease that forms run-on oligomer filaments when activated and possesses both accelerated DNA cleavage activity and expanded DNA sequence specificity. Mutations disrupting the run-on oligomer filament eliminate the robust antiphage activity of wild-type SgrAI, and the observation that even relatively modest disruptions completely abolish this anti-viral activity shows that the greater speed imparted by the run-on oligomer filament mechanism is critical to its biological function. Simulations of DNA cleavage by SgrAI uncover the origins of the kinetic advantage of this newly described mechanism of enzyme regulation over more conventional mechanisms, as well as the origin of the sequestering effect responsible for the protection of the host genome against damaging DNA cleavage activity of activated SgrAI.IMPORTANCE This work is motivated by an interest in understanding the characteristics and advantages of a relatively newly discovered enzyme mechanism involving filament formation. SgrAI is an enzyme responsible for protecting against viral infections in its host bacterium and was one of the first such enzymes shown to utilize such a mechanism. In this work, filament formation by SgrAI is disrupted, and the effects on the speed of the purified enzyme as well as its function in cells are measured. It was found that even small disruptions, which weaken but do not destroy filament formation, eliminate the ability of SgrAI to protect cells from viral infection, its normal biological function. Simulations of enzyme activity were also performed and show how filament formation can greatly speed up an enzyme's activation compared to that of other known mechanisms, as well as to better localize its action to molecules of interest, such as invading phage DNA.
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Affiliation(s)
- Claudia J Barahona
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - L Emilia Basantes
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Kassidy J Tompkins
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Desirae M Heitman
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Barbara I Chukwu
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Juan Sanchez
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Jonathan L Sanchez
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Niloofar Ghadirian
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Chad K Park
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - N C Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
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7
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Shen BW, Doyle L, Bradley P, Heiter DF, Lunnen KD, Wilson GG, Stoddard BL. Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI. Nucleic Acids Res 2019; 47:450-467. [PMID: 30395313 PMCID: PMC6326814 DOI: 10.1093/nar/gky1059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/15/2018] [Accepted: 10/17/2018] [Indexed: 11/17/2022] Open
Abstract
BbvCI, a Type IIT restriction endonuclease, recognizes and cleaves the seven base pair sequence 5'-CCTCAGC-3', generating 3-base, 5'-overhangs. BbvCI is composed of two protein subunits, each containing one catalytic site. Either site can be inactivated by mutation resulting in enzyme variants that nick DNA in a strand-specific manner. Here we demonstrate that the holoenzyme is labile, with the R1 subunit dissociating at low pH. Crystallization of the R2 subunit under such conditions revealed an elongated dimer with the two catalytic sites located on opposite sides. Subsequent crystallization at physiological pH revealed a tetramer comprising two copies of each subunit, with a pair of deep clefts each containing two catalytic sites appropriately positioned and oriented for DNA cleavage. This domain organization was further validated with single-chain protein constructs in which the two enzyme subunits were tethered via peptide linkers of variable length. We were unable to crystallize a DNA-bound complex; however, structural similarity to previously crystallized restriction endonucleases facilitated creation of an energy-minimized model bound to DNA, and identification of candidate residues responsible for target recognition. Mutation of residues predicted to recognize the central C:G base pair resulted in an altered enzyme that recognizes and cleaves CCTNAGC (N = any base).
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Affiliation(s)
- Betty W Shen
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Lindsey Doyle
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Phil Bradley
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Daniel F Heiter
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Keith D Lunnen
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | | | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
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8
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Alcala-Torano R, Walther M, Sommer DJ, Park CK, Ghirlanda G. Rational design of a hexameric protein assembly stabilized by metal chelation. Biopolymers 2018; 109:e23233. [PMID: 30191549 DOI: 10.1002/bip.23233] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 06/15/2018] [Accepted: 07/05/2018] [Indexed: 12/27/2022]
Abstract
Protein-based self-assembled nanostructures hold tremendous promise as smart materials. One strategy to control the assembly of individual protein modules takes advantage of the directionality and high affinity bonding afforded by metal chelation. Here, we describe the use of 2,2'-bipyridine units (Bpy) as side chains to template the assembly of large structures (MW approx. 35 000 Da) in a metal-dependent manner. The structures are trimers of independently folded 3-helix bundles, and are held together by 2 Me(Bpy)3 complexes. The assemblies are stable to thermal denaturation, and are more than 90% helical at 90°C. Circular dichroism spectroscopy shows that one of the 2 possible (Bpy)3 enantiomers is favored over the other. Because of the sequence pliability of the starting peptides, these constructs could find use to organize functional groups at controlled positions within a supramolecular assembly.
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Affiliation(s)
| | - Mathieu Walther
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
| | - Dayn J Sommer
- School of Molecular Sciences, Arizona State University, Tempe, Arizona
| | - Chad K Park
- Department of Biochemistry, University of Arizona, Tucson, Arizona
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9
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Park CK, Sanchez JL, Barahona C, Basantes LE, Sanchez J, Hernandez C, Horton NC. The run-on oligomer filament enzyme mechanism of SgrAI: Part 1. Assembly kinetics of the run-on oligomer filament. J Biol Chem 2018; 293:14585-14598. [PMID: 30068553 DOI: 10.1074/jbc.ra118.003680] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/30/2018] [Indexed: 01/06/2023] Open
Abstract
Filament or run-on oligomer formation by metabolic enzymes is now recognized as a widespread phenomenon having potentially unique enzyme regulatory properties and biological roles, and its dysfunction is implicated in human diseases such as cancer, diabetes, and developmental disorders. SgrAI is a bacterial allosteric type II restriction endonuclease that binds to invading phage DNA, may protect the host DNA from off-target cleavage activity, and forms run-on oligomeric filaments with enhanced DNA-cleavage activity and altered DNA sequence specificity. However, the mechanisms of SgrAI filament growth, cooperativity in filament formation, sequestration of enzyme activity, and advantages over other filament mechanisms remain unknown. In this first of a two-part series, we developed methods and models to derive association and dissociation rate constants of DNA-bound SgrAI in run-on oligomers and addressed the specific questions of cooperativity and filament growth mechanisms. We show that the derived rate constants are consistent with the run-on oligomer sizes determined by EM analysis and are most consistent with a noncooperative growth mode of the run-on oligomer. These models and methods are extended in the accompanying article to include the full DNA-cleavage pathway and address specific questions related to the run-on oligomer mechanism including the sequestration of DNA-cleavage activity and trapping of products.
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Affiliation(s)
- Chad K Park
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Jonathan L Sanchez
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Claudia Barahona
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - L Emilia Basantes
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Juan Sanchez
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Christian Hernandez
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - N C Horton
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
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10
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Park CK, Sanchez JL, Barahona C, Basantes LE, Sanchez J, Hernandez C, Horton NC. The run-on oligomer filament enzyme mechanism of SgrAI: Part 2. Kinetic modeling of the full DNA cleavage pathway. J Biol Chem 2018; 293:14599-14615. [PMID: 30054273 DOI: 10.1074/jbc.ra118.003682] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/17/2018] [Indexed: 11/06/2022] Open
Abstract
Filament or run-on oligomer formation by enzymes is now recognized as a widespread phenomenon with potentially unique enzyme regulatory properties and biological roles. SgrAI is an allosteric type II restriction endonuclease that forms run-on oligomeric filaments with activated DNA cleavage activity and altered DNA sequence specificity. In this two-part work, we measure individual steps in the run-on oligomer filament mechanism to address specific questions of cooperativity, trapping, filament growth mechanisms, and sequestration of activity using fluorophore-labeled DNA, kinetic FRET measurements, and reaction modeling with global data fitting. The final models and rate constants show that the assembly step involving association of SgrAI-DNA complexes into the run-on oligomer filament is relatively slow (3-4 orders of magnitude slower than diffusion limited) and rate-limiting at low to moderate concentrations of SgrAI-DNA. The disassembly step involving dissociation of complexes of SgrAI-DNA from each other in the run-on oligomer filament is the next slowest step but is fast enough to limit the residence time of any one copy of SgrAI or DNA within the dynamic filament. Further, the rate constant for DNA cleavage is found to be 4 orders of magnitude faster in the run-on oligomer filament than in isolated SgrAI-DNA complexes and faster than dissociation of SgrAI-DNA complexes from the run-on oligomer filament, making the reaction efficient in that each association into the filament likely leads to DNA cleavage before filament dissociation.
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Affiliation(s)
- Chad K Park
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Jonathan L Sanchez
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Claudia Barahona
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - L Emilia Basantes
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Juan Sanchez
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - Christian Hernandez
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
| | - N C Horton
- From the Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona 85721
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11
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Sanchez JL, Romero Z, Quinones A, Torgeson KR, Horton NC. DNA Binding and Cleavage by the Human Parvovirus B19 NS1 Nuclease Domain. Biochemistry 2016; 55:6577-6593. [PMID: 27809499 DOI: 10.1021/acs.biochem.6b00534] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Infection with human parvovirus B19 (B19V) has been associated with a myriad of illnesses, including erythema infectiosum (Fifth disease), hydrops fetalis, arthropathy, hepatitis, and cardiomyopathy, and also possibly the triggering of any number of different autoimmune diseases. B19V NS1 is a multidomain protein that plays a critical role in viral replication, with predicted nuclease, helicase, and gene transactivation activities. Herein, we investigate the biochemical activities of the nuclease domain (residues 2-176) of B19V NS1 (NS1-nuc) in sequence-specific DNA binding of the viral origin of replication sequences, as well as those of promoter sequences, including the viral p6 and the human p21, TNFα, and IL-6 promoters previously identified in NS1-dependent transcriptional transactivation. NS1-nuc was found to bind with high cooperativity and with multiple (five to seven) copies to the NS1 binding elements (NSBE) found in the viral origin of replication and the overlapping viral p6 promoter DNA sequence. NS1-nuc was also found to bind cooperatively with at least three copies to the GC-rich Sp1 binding sites of the human p21 gene promoter. Only weak or nonspecific binding of NS1-nuc to the segments of the TNFα and IL-6 promoters was found. Cleavage of DNA by NS1-nuc occurred at the expected viral sequence (the terminal resolution site), but only in single-stranded DNA, and NS1-nuc was found to covalently attach to the 5' end of the DNA at the cleavage site. Off-target cleavage by NS1-nuc was also identified.
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Affiliation(s)
- Jonathan L Sanchez
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | - Zachary Romero
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States.,Undergraduate Research Opportunities Consortium-Minorities Health Disparity Program (UROC-MHD), University of Arizona Graduate College, University of Arizona , Tucson, Arizona 85721, United States
| | - Angelica Quinones
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States.,Undergraduate Research Opportunities Consortium-Minorities Health Disparity Program (UROC-MHD), University of Arizona Graduate College, University of Arizona , Tucson, Arizona 85721, United States.,BUILDing SCHOLARS Program, University of Texas at El Paso , El Paso, Texas 79968, United States
| | - Kristiane R Torgeson
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
| | - Nancy C Horton
- Department of Chemistry and Biochemistry, University of Arizona , Tucson, Arizona 85721, United States
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12
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Tamulaitis G, Rutkauskas M, Zaremba M, Grazulis S, Tamulaitiene G, Siksnys V. Functional significance of protein assemblies predicted by the crystal structure of the restriction endonuclease BsaWI. Nucleic Acids Res 2015; 43:8100-10. [PMID: 26240380 PMCID: PMC4652773 DOI: 10.1093/nar/gkv768] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Accepted: 07/17/2015] [Indexed: 02/03/2023] Open
Abstract
Type II restriction endonuclease BsaWI recognizes a degenerated sequence 5′-W/CCGGW-3′ (W stands for A or T, ‘/’ denotes the cleavage site). It belongs to a large family of restriction enzymes that contain a conserved CCGG tetranucleotide in their target sites. These enzymes are arranged as dimers or tetramers, and require binding of one, two or three DNA targets for their optimal catalytic activity. Here, we present a crystal structure and biochemical characterization of the restriction endonuclease BsaWI. BsaWI is arranged as an ‘open’ configuration dimer and binds a single DNA copy through a minor groove contacts. In the crystal primary BsaWI dimers form an indefinite linear chain via the C-terminal domain contacts implying possible higher order aggregates. We show that in solution BsaWI protein exists in a dimer-tetramer-oligomer equilibrium, but in the presence of specific DNA forms a tetramer bound to two target sites. Site-directed mutagenesis and kinetic experiments show that BsaWI is active as a tetramer and requires two target sites for optimal activity. We propose BsaWI mechanism that shares common features both with dimeric Ecl18kI/SgrAI and bona fide tetrameric NgoMIV/SfiI enzymes.
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Affiliation(s)
- Gintautas Tamulaitis
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Marius Rutkauskas
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Mindaugas Zaremba
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Saulius Grazulis
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Giedre Tamulaitiene
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Virginijus Siksnys
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
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13
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Shah S, Sanchez J, Stewart A, Piperakis MM, Cosstick R, Nichols C, Park CK, Ma X, Wysocki V, Bitinaite J, Horton NC. Probing the run-on oligomer of activated SgrAI bound to DNA. PLoS One 2015; 10:e0124783. [PMID: 25880668 PMCID: PMC4399878 DOI: 10.1371/journal.pone.0124783] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Accepted: 03/05/2015] [Indexed: 02/04/2023] Open
Abstract
SgrAI is a type II restriction endonuclease with an unusual mechanism of activation involving run-on oligomerization. The run-on oligomer is formed from complexes of SgrAI bound to DNA containing its 8 bp primary recognition sequence (uncleaved or cleaved), and also binds (and thereby activates for DNA cleavage) complexes of SgrAI bound to secondary site DNA sequences which contain a single base substitution in either the 1st/8th or the 2nd/7th position of the primary recognition sequence. This modulation of enzyme activity via run-on oligomerization is a newly appreciated phenomenon that has been shown for a small but increasing number of enzymes. One outstanding question regarding the mechanistic model for SgrAI is whether or not the activating primary site DNA must be cleaved by SgrAI prior to inducing activation. Herein we show that an uncleavable primary site DNA containing a 3'-S-phosphorothiolate is in fact able to induce activation. In addition, we now show that cleavage of secondary site DNA can be activated to nearly the same degree as primary, provided a sufficient number of flanking base pairs are present. We also show differences in activation and cleavage of the two types of secondary site, and that effects of selected single site substitutions in SgrAI, as well as measured collisional cross-sections from previous work, are consistent with the cryo-electron microscopy model for the run-on activated oligomer of SgrAI bound to DNA.
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Affiliation(s)
- Santosh Shah
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, United States of America
| | - Jonathan Sanchez
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, United States of America
| | - Andrew Stewart
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, United States of America
- Genetics Graduate Program, University of Arizona, Tucson, AZ 85721, United States of America
| | - Michael M. Piperakis
- Department of Chemistry, University of Liverpool, Liverpool, United Kingdom, L69 7ZD, United States of America
| | - Richard Cosstick
- Department of Chemistry, University of Liverpool, Liverpool, United Kingdom, L69 7ZD, United States of America
| | - Claire Nichols
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, United States of America
| | - Chad K. Park
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, United States of America
| | - Xin Ma
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, United States of America
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, United States of America
| | - Vicki Wysocki
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, United States of America
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH 43210, United States of America
| | - Jurate Bitinaite
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, United States of America
| | - Nancy C. Horton
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721, United States of America
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14
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Lyumkis D, Talley H, Stewart A, Shah S, Park CK, Tama F, Potter CS, Carragher B, Horton NC. Allosteric regulation of DNA cleavage and sequence-specificity through run-on oligomerization. Structure 2013; 21:1848-58. [PMID: 24055317 PMCID: PMC3898938 DOI: 10.1016/j.str.2013.08.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 08/08/2013] [Accepted: 08/09/2013] [Indexed: 10/26/2022]
Abstract
SgrAI is a sequence specific DNA endonuclease that functions through an unusual enzymatic mechanism that is allosterically activated 200- to 500-fold by effector DNA, with a concomitant expansion of its DNA sequence specificity. Using single-particle transmission electron microscopy to reconstruct distinct populations of SgrAI oligomers, we show that in the presence of allosteric, activating DNA, the enzyme forms regular, repeating helical structures characterized by the addition of DNA-binding dimeric SgrAI subunits in a run-on manner. We also present the structure of oligomeric SgrAI at 8.6 Å resolution, demonstrating the conformational state of SgrAI in its activated form. Activated and oligomeric SgrAI displays key protein-protein interactions near the helix axis between its N termini, as well as allosteric protein-DNA interactions that are required for enzymatic activation. The hybrid approach reveals an unusual mechanism of enzyme activation that explains SgrAI's oligomerization and allosteric behavior.
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Affiliation(s)
- Dmitry Lyumkis
- National Resource for Automated Molecular Microscopy, The Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037
| | - Heather Talley
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721
| | - Andrew Stewart
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721
- Genetics Interdisciplinary Graduate Program, University of Arizona, Tucson, AZ, 85721
| | - Santosh Shah
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721
| | - Chad K. Park
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721
| | - Florence Tama
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721
| | - Clinton S. Potter
- National Resource for Automated Molecular Microscopy, The Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037
| | - Bridget Carragher
- National Resource for Automated Molecular Microscopy, The Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037
| | - Nancy C. Horton
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, 85721
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15
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Ma X, Shah S, Zhou M, Park CK, Wysocki VH, Horton NC. Structural analysis of activated SgrAI-DNA oligomers using ion mobility mass spectrometry. Biochemistry 2013; 52:4373-81. [PMID: 23742104 DOI: 10.1021/bi3013214] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
SgrAI is a type IIF restriction endonuclease that cuts an unusually long recognition sequence and exhibits self-modulation of DNA cleavage activity and sequence specificity. Previous studies have shown that SgrAI forms large oligomers when bound to particular DNA sequences and under the same conditions where SgrAI exhibits accelerated DNA cleavage kinetics. However, the detailed structure and stoichiometry of the SgrAI-DNA complex as well as the basic building block of the oligomers have not been fully characterized. Ion mobility mass spectrometry (IM-MS) was employed to analyze SgrAI-DNA complexes and show that the basic building block of the oligomers is the DNA-bound SgrAI dimer (DBD) with one SgrAI dimer bound to two precleaved duplex DNA molecules each containing one-half of the SgrAI primary recognition sequence. The oligomers contain variable numbers of DBDs with as many as 19 DBDs. Observation of the large oligomers shows that nanoelectrospray ionization (nano-ESI) can preserve the proposed activated form of an enzyme. Finally, the collision cross section of the SgrAI-DNA oligomers measured by IM-MS was found to have a linear relationship with the number of DBDs in each oligomer, suggesting a regular, repeating structure.
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Affiliation(s)
- Xin Ma
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
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16
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Briggs DB, Giron RM, Schnittker K, Hart MV, Park CK, Hausrath AC, Tsao TS. Zinc enhances adiponectin oligomerization to octadecamers but decreases the rate of disulfide bond formation. Biometals 2012; 25:469-86. [PMID: 22234497 DOI: 10.1007/s10534-012-9519-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 12/30/2011] [Indexed: 12/31/2022]
Abstract
Adiponectin, a hormone secreted from adipocytes, has been shown to protect against development of insulin resistance, ischemia-reperfusion injury, and inflammation. Adiponectin assembles into multiple oligomeric isoforms: trimers, hexamers and several higher molecular weight (HMW) species. Of these, the HMW species are selectively decreased during the onset of type 2 diabetes. Despite the critical role of HMW adiponectin in insulin responsiveness, its assembly process is poorly understood. In this report, we investigated the role of divalent cations in adiponectin assembly. Purified adiponectin 18mers, the largest HMW species, did not collapse to smaller oligomers after treatment with high concentrations of EDTA. However, treatment with EDTA or another chelator DTPA inhibited the oligomerization of 18mers from trimers in vitro. Zn(2+) specifically increased the formation of 18mers when compared with Cu(2+), Mg(2+), and Ca(2+). Distribution of adiponectin oligomers secreted from zinc chelator TPEN-treated rat adipocytes skewed toward increased proportions of hexamers and trimers. While we observed presence of zinc in adiponectin purified from calf serum, the role of zinc in disulfide bonding between oligomers was examined because the process is critical for 18mer assembly. Surprisingly, Zn(2+) inhibited disulfide bond formation early in the oligomerization process. We hypothesize that initial decreases in disulfide formation rates could allow adiponectin subunits to associate before becoming locked in fully oxidized conformations incapable of further oligomerization. These data demonstrate that zinc stimulates oligomerization of HMW adiponectin and possibly other disulfide-dependent protein assembly processes.
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Affiliation(s)
- David B Briggs
- Department of Chemistry and Biochemistry, University of Arizona, MRB Diabetes Research, Tucson, AZ 85724, USA
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17
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Little EJ, Dunten PW, Bitinaite J, Horton NC. New clues in the allosteric activation of DNA cleavage by SgrAI: structures of SgrAI bound to cleaved primary-site DNA and uncleaved secondary-site DNA. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2011; 67:67-74. [PMID: 21206063 PMCID: PMC3016018 DOI: 10.1107/s0907444910047785] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Accepted: 11/17/2010] [Indexed: 11/10/2022]
Abstract
SgrAI is a type II restriction endonuclease that cuts an unusually long recognition sequence and exhibits allosteric self-activation with expansion of DNA-sequence specificity. The three-dimensional crystal structures of SgrAI bound to cleaved primary-site DNA and Mg²(+) and bound to secondary-site DNA with either Mg²(+) or Ca²(+) are presented. All three structures show a conformation of enzyme and DNA similar to the previously determined dimeric structure of SgrAI bound to uncleaved primary-site DNA and Ca²(+) [Dunten et al. (2008), Nucleic Acids Res. 36, 5405-5416], with the exception of the cleaved bond and a slight shifting of the DNA in the SgrAI/cleaved primary-site DNA/Mg²(+) structure. In addition, a new metal ion binding site is located in one of the two active sites in this structure, which is consistent with proposals for the existence of a metal-ion site near the 3'-O leaving group.
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Affiliation(s)
- Elizabeth J. Little
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
| | - Pete W. Dunten
- Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, CA 94025, USA
| | | | - Nancy C. Horton
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA
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18
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Park CK, Joshi HK, Agrawal A, Ghare MI, Little EJ, Dunten PW, Bitinaite J, Horton NC. Domain swapping in allosteric modulation of DNA specificity. PLoS Biol 2010; 8:e1000554. [PMID: 21151881 PMCID: PMC2998434 DOI: 10.1371/journal.pbio.1000554] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2010] [Accepted: 10/27/2010] [Indexed: 11/19/2022] Open
Abstract
SgrAI is a type IIF restriction endonuclease that cuts an unusually long recognition sequence and exhibits allosteric self-modulation of cleavage activity and sequence specificity. Previous studies have shown that DNA bound dimers of SgrAI oligomerize into an activated form with higher DNA cleavage rates, although previously determined crystal structures of SgrAI bound to DNA show only the DNA bound dimer. A new crystal structure of the type II restriction endonuclease SgrAI bound to DNA and Ca(2+) is now presented, which shows the close association of two DNA bound SgrAI dimers. This tetrameric form is unlike those of the homologous enzymes Cfr10I and NgoMIV and is formed by the swapping of the amino-terminal 24 amino acid residues. Two mutations predicted to destabilize the swapped form of SgrAI, P27W and P27G, have been made and shown to eliminate both the oligomerization of the DNA bound SgrAI dimers as well as the allosteric stimulation of DNA cleavage by SgrAI. A mechanism involving domain swapping is proposed to explain the unusual allosteric properties of SgrAI via association of the domain swapped tetramer of SgrAI bound to DNA into higher order oligomers.
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Affiliation(s)
- Chad K. Park
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, United States of America
| | - Hemant K. Joshi
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, United States of America
| | - Alka Agrawal
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
| | - M. Imran Ghare
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, United States of America
| | - Elizabeth J. Little
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, United States of America
| | - Pete W. Dunten
- Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California, United States of America
| | - Jurate Bitinaite
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
| | - Nancy C. Horton
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, United States of America
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