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Liu X, Ma S. Recent Development of Glucosamine‐6‐phosphate Derivatives as Potential Antibacterial Agents. ChemistrySelect 2020. [DOI: 10.1002/slct.201904075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Xingbang Liu
- Department of Medicinal Chemistry Key Laboratory of Chemical Biology (Ministry of Education) School of Pharmaceutical SciencesShandong University 44 West Culture Road Jinan 250012 P.R. China
| | - Shutao Ma
- Department of Medicinal Chemistry Key Laboratory of Chemical Biology (Ministry of Education) School of Pharmaceutical SciencesShandong University 44 West Culture Road Jinan 250012 P.R. China
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Seith DD, Bingaman JL, Veenis AJ, Button AC, Bevilacqua PC. Elucidation of Catalytic Strategies of Small Nucleolytic Ribozymes From Comparative Analysis of Active Sites. ACS Catal 2018; 8:314-327. [PMID: 32547833 PMCID: PMC7296830 DOI: 10.1021/acscatal.7b02976] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A number of small, self-cleaving ribozyme classes have been identified including the hammerhead, hairpin, hepatitis delta virus (HDV), Varkud satellite (VS), glmS, twister, hatchet, pistol, and twister sister ribozymes. Within the active sites of these ribozymes, myriad functional groups contribute to catalysis. There has been extensive structure-function analysis of individual ribozymes, but the extent to which catalytic devices are shared across different ribozyme classes is unclear. As such, emergent catalytic principles for ribozymes may await discovery. Identification of conserved catalytic devices can deepen our understanding of RNA catalysis specifically and of enzymic catalysis generally. To probe similarities and differences amongst ribozyme classes, active sites from more than 80 high-resolution crystal structures of self-cleaving ribozymes were compared computationally. We identify commonalities amongst ribozyme classes pertaining to four classic catalytic devices: deprotonation of the 2'OH nucleophile (γ), neutralization of the non-bridging oxygens of the scissile phosphate (β), neutralization of the O5' leaving group (δ), and in-line nucleophilic attack (α). In addition, we uncover conservation of two catalytic devices, each of which centers on the activation of the 2'OH nucleophile by a guanine: one to acidify the 2'OH by hydrogen bond donation to it (γ') and one to acidify the 2'OH by releasing it from non-productive interactions by competitive hydrogen bonding (γ''). Our findings reveal that the amidine functionalities of G, A, and C are especially important for these strategies, and help explain absence of U at ribozyme active sites. The identified γ' and γ'' catalytic strategies help unify the catalytic strategies shared amongst catalytic RNAs and may be important for large ribozymes, as well as protein enzymes that act on nucleic acids.
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Affiliation(s)
- Daniel D. Seith
- Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
- These two authors contributed equally to this work
| | - Jamie L. Bingaman
- Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
- These two authors contributed equally to this work
| | - Andrew J. Veenis
- Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
| | - Aileen C. Button
- Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Biochemistry, The University of Vermont, Burlington, Vermont 05405
| | - Philip C. Bevilacqua
- Department of Chemistry and Center for RNA Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802
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Bingaman JL, Zhang S, Stevens DR, Yennawar NH, Hammes-Schiffer S, Bevilacqua PC. The GlcN6P cofactor plays multiple catalytic roles in the glmS ribozyme. Nat Chem Biol 2017; 13:439-445. [PMID: 28192411 PMCID: PMC5362308 DOI: 10.1038/nchembio.2300] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Accepted: 12/09/2016] [Indexed: 01/06/2023]
Abstract
RNA enzymes (ribozymes) have remarkably diverse biological roles despite having limited chemical diversity. Protein enzymes enhance their reactivity through recruitment of cofactors; likewise, the naturally occurring glmS ribozyme uses the glucosamine-6-phosphate (GlcN6P) organic cofactor for phosphodiester bond cleavage. Prior structural and biochemical studies have implicated GlcN6P as the general acid. Here we describe new catalytic roles of GlcN6P through experiments and calculations. Large stereospecific normal thio effects and a lack of metal-ion rescue in the holoribozyme indicate that nucleobases and the cofactor play direct chemical roles and align the active site for self-cleavage. Large stereospecific inverse thio effects in the aporibozyme suggest that the GlcN6P cofactor disrupts an inhibitory interaction of the nucleophile. Strong metal-ion rescue in the aporibozyme reveals that this cofactor also provides electrostatic stabilization. Ribozyme organic cofactors thus perform myriad catalytic roles, thereby allowing RNA to compensate for its limited functional diversity.
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Affiliation(s)
- Jamie L. Bingaman
- Department of Chemistry and Center for RNA Molecular
Biology, The Pennsylvania State University, University Park, Pennsylvania 16802,
United States
| | - Sixue Zhang
- Department of Chemistry, University of Illinois at
Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - David R. Stevens
- Department of Chemistry, University of Illinois at
Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Neela H. Yennawar
- X-ray Crystallography Facility, Huck Institutes of the Life
Sciences, The Pennsylvania State University, 8 Althouse Laboratory, University Park,
Pennsylvania 16802, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, University of Illinois at
Urbana-Champaign, 600 South Mathews Avenue, Urbana, Illinois 61801, United
States
| | - Philip C. Bevilacqua
- Department of Chemistry and Center for RNA Molecular
Biology, The Pennsylvania State University, University Park, Pennsylvania 16802,
United States
- Department of Biochemistry and Molecular Biology, The
Pennsylvania State University, University Park, Pennsylvania 16802, United
States
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Fei X, Holmes T, Diddle J, Hintz L, Delaney D, Stock A, Renner D, McDevitt M, Berkowitz DB, Soukup JK. Phosphatase-inert glucosamine 6-phosphate mimics serve as actuators of the glmS riboswitch. ACS Chem Biol 2014; 9:2875-82. [PMID: 25254431 PMCID: PMC4273988 DOI: 10.1021/cb500458f] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
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The glmS riboswitch is unique among gene-regulating
riboswitches and catalytic RNAs. This is because its own metabolite,
glucosamine-6-phosphate (GlcN6P), binds to the riboswitch and catalytically
participates in the RNA self-cleavage reaction, thereby providing
a novel negative feedback mechanism. Given that a number of pathogens
harbor the glmS riboswitch, artificial actuators
of this potential RNA target are of great interest. Structural/kinetic
studies point to the 2-amino and 6-phosphate ester functionalities
in GlcN6P as being crucial for this actuation. As a first step toward
developing artificial actuators, we have synthesized a series of nine
GlcN6P analogs bearing phosphatase-inert surrogates in place of the
natural phosphate ester. Self-cleavage assays with the Bacillus cereusglmS riboswitch
give a broad SAR. Two analogs display significant activity, namely,
the 6-deoxy-6-phosphonomethyl analog (5) and the 6-O-malonyl ether (13). Kinetic profiles show
a 22-fold and a 27-fold higher catalytic efficiency, respectively,
for these analogs vs glucosamine (GlcN). Given their nonhydrolyzable
phosphate surrogate functionalities, these analogs are arguably the
most robust artificial glmS riboswitch actuators
yet reported. Interestingly, the malonyl ether (13, extra
O atom) is much more effective than the simple malonate (17), and the “sterically true” phosphonate (5) is far superior to the chain-truncated (7) or chain-extended
(11) analogs, suggesting that positioning via Mg coordination
is important for activity. Docking results are consistent with this
view. Indeed, the viability of the phosphonate and 6-O-malonyl ether
mimics of GlcN6P points to a potential new strategy for artificial
actuation of the glmS riboswitch in a biological
setting, wherein phosphatase-resistance is paramount.
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Affiliation(s)
- Xiang Fei
- Department
of Chemistry, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - Thomas Holmes
- Department
of Chemistry, Creighton University, Omaha, Nebraska 68178, United States
| | - Julianna Diddle
- Department
of Chemistry, Creighton University, Omaha, Nebraska 68178, United States
| | - Lauren Hintz
- Department
of Chemistry, Creighton University, Omaha, Nebraska 68178, United States
| | - Dan Delaney
- Department
of Chemistry, Creighton University, Omaha, Nebraska 68178, United States
| | - Alex Stock
- Department
of Chemistry, Creighton University, Omaha, Nebraska 68178, United States
| | - Danielle Renner
- Department
of Chemistry, Creighton University, Omaha, Nebraska 68178, United States
| | - Molly McDevitt
- Department
of Chemistry, Creighton University, Omaha, Nebraska 68178, United States
| | - David B. Berkowitz
- Department
of Chemistry, University of Nebraska, Lincoln, Nebraska 68588, United States
| | - Juliane K. Soukup
- Department
of Chemistry, Creighton University, Omaha, Nebraska 68178, United States
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