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Tillault AS, Schultz SK, Wieden HJ, Kothe U. Molecular Determinants for 23S rRNA Recognition and Modification by the E. coli Pseudouridine Synthase RluE. J Mol Biol 2018; 430:1284-1294. [PMID: 29555553 DOI: 10.1016/j.jmb.2018.03.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/25/2018] [Accepted: 03/13/2018] [Indexed: 11/18/2022]
Abstract
The isomerization of uridine to pseudouridine is the most common type of RNA modification found in RNAs across all domains of life and is performed by RNA-dependent and RNA-independent enzymes. The Escherichia coli pseudouridine synthase RluE acts as a stand-alone, highly specific enzyme forming the universally conserved pseudouridine at position 2457, located in helix 89 (H89) of the 23S rRNA in the peptidyltransferase center. Here, we conduct a detailed structure-function analysis to determine the structural elements both in RluE and in 23S rRNA required for RNA-protein interaction and pseudouridine formation. We determined that RluE recognizes a large part of 23S rRNA comprising both H89 and the single-stranded flanking regions which explains the high substrate specificity of RluE. Within RluE, the target RNA is recognized through sequence-specific contacts with loop L7-8 as well as interactions with loop L1-2 and the flexible N-terminal region. We demonstrate that RluE is a faster pseudouridine synthase than other enzymes which likely enables it to act in the early stages of ribosome formation. In summary, our biochemical characterization of RluE provides detailed insight into the molecular mechanism of RluE forming a highly conserved pseudouridine during ribosome biogenesis.
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Affiliation(s)
- Anne-Sophie Tillault
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Sarah K Schultz
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Hans-Joachim Wieden
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada
| | - Ute Kothe
- Alberta RNA Research and Training Institute, Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB, T1K 3M4, Canada.
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2
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Kim MH, Lee BH, Kim MK. Robust elastic network model: A general modeling for precise understanding of protein dynamics. J Struct Biol 2015; 190:338-47. [PMID: 25891099 DOI: 10.1016/j.jsb.2015.04.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 04/07/2015] [Accepted: 04/09/2015] [Indexed: 01/30/2023]
Abstract
In the study of protein dynamics relevant to functions, normal mode analysis based on elastic network models (ENMs) has become popular. These models are usually validated by comparing the calculated atomic fluctuation for a single protein in a vacuum to experimental temperature factors in the crystal packing state. Without reflecting the crystal packing effect, in addition, their arbitrary assignment of spring constants leads to inaccurate simulation results, yielding a low correlation of the B-factor. To overcome this limitation, we propose a robust elastic network model (RENM) that not only considers the crystalline effect by using symmetric constraint information but also uses lumped masses and specific spring constants based on the type of amino acids and chemical interactions, respectively. Simulation results with more than 500 protein structures verify qualitatively and quantitatively that one can obtain the better correlation of the B-factor by RENM without additional computational burden. Moreover, an optimal spring constant in physical units (dyne/cm) is quantitatively determined as a function of the temperature at 100 and 290K, which enables us to predict the atomic fluctuations and vibrational density of states (VDOS) without a fitting process. The additional investigation of 80 high-resolution crystal structures with anisotropic displacement parameters (ADPs) indicates that RENM could give a full description of vibrational characteristics of individual residues in proteins.
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Affiliation(s)
- Min Hyeok Kim
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 440-746, South Korea
| | - Byung Ho Lee
- School of Mechanical Engineering, Sungkyunkwan University, Suwon 440-746, South Korea
| | - Moon Ki Kim
- SKKU Advanced Institute of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 440-746, South Korea; School of Mechanical Engineering, Sungkyunkwan University, Suwon 440-746, South Korea.
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Huet T, Miannay FA, Patton JR, Thore S. Steroid receptor RNA activator (SRA) modification by the human pseudouridine synthase 1 (hPus1p): RNA binding, activity, and atomic model. PLoS One 2014; 9:e94610. [PMID: 24722331 PMCID: PMC3983220 DOI: 10.1371/journal.pone.0094610] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 03/18/2014] [Indexed: 11/23/2022] Open
Abstract
The most abundant of the modified nucleosides, and once considered as the “fifth” nucleotide in RNA, is pseudouridine, which results from the action of pseudouridine synthases. Recently, the mammalian pseudouridine synthase 1 (hPus1p) has been reported to modulate class I and class II nuclear receptor responses through its ability to modify the Steroid receptor RNA Activator (SRA). These findings highlight a new level of regulation in nuclear receptor (NR)-mediated transcriptional responses. We have characterised the RNA association and activity of the human Pus1p enzyme with its unusual SRA substrate. We validate that the minimal RNA fragment within SRA, named H7, is necessary for both the association and modification by hPus1p. Furthermore, we have determined the crystal structure of the catalytic domain of hPus1p at 2.0 Å resolution, alone and in a complex with several molecules present during crystallisation. This model shows an extended C-terminal helix specifically found in the eukaryotic protein, which may prevent the enzyme from forming a homodimer, both in the crystal lattice and in solution. Our biochemical and structural data help to understand the hPus1p active site architecture, and detail its particular requirements with regard to one of its nuclear substrates, the non-coding RNA SRA.
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Affiliation(s)
- Tiphaine Huet
- Department of Molecular Biology, University of Geneva, Sciences III, Geneva, Switzerland
| | | | - Jeffrey R. Patton
- Department of Pathology, Microbiology and Immunology, University of South Carolina, School of Medicine, Columbia, South Carolina, United States of America
| | - Stéphane Thore
- Department of Molecular Biology, University of Geneva, Sciences III, Geneva, Switzerland
- * E-mail:
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Czudnochowski N, Wang AL, Finer-Moore J, Stroud RM. In human pseudouridine synthase 1 (hPus1), a C-terminal helical insert blocks tRNA from binding in the same orientation as in the Pus1 bacterial homologue TruA, consistent with their different target selectivities. J Mol Biol 2013; 425:3875-87. [PMID: 23707380 DOI: 10.1016/j.jmb.2013.05.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 05/11/2013] [Accepted: 05/17/2013] [Indexed: 10/26/2022]
Abstract
Human pseudouridine (Ψ) synthase Pus1 (hPus1) modifies specific uridine residues in several non-coding RNAs: tRNA, U2 spliceosomal RNA, and steroid receptor activator RNA. We report three structures of the catalytic core domain of hPus1 from two crystal forms, at 1.8Å resolution. The structures are the first of a mammalian Ψ synthase from the set of five Ψ synthase families common to all kingdoms of life. hPus1 adopts a fold similar to bacterial Ψ synthases, with a central antiparallel β-sheet flanked by helices and loops. A flexible hinge at the base of the sheet allows the enzyme to open and close around an electropositive active-site cleft. In one crystal form, a molecule of Mes [2-(N-morpholino)ethane sulfonic acid] mimics the target uridine of an RNA substrate. A positively charged electrostatic surface extends from the active site towards the N-terminus of the catalytic domain, suggesting an extensive binding site specific for target RNAs. Two α-helices C-terminal to the core domain, but unique to hPus1, extend along the back and top of the central β-sheet and form the walls of the RNA binding surface. Docking of tRNA to hPus1 in a productive orientation requires only minor conformational changes to enzyme and tRNA. The docked tRNA is bound by the electropositive surface of the protein employing a completely different binding mode than that seen for the tRNA complex of the Escherichia coli homologue TruA.
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Affiliation(s)
- Nadine Czudnochowski
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
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Zhou J, Liang B, Li H. Functional and structural impact of target uridine substitutions on the H/ACA ribonucleoprotein particle pseudouridine synthase. Biochemistry 2010; 49:6276-81. [PMID: 20575532 PMCID: PMC2928259 DOI: 10.1021/bi1006699] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Box H/ACA ribonucleoprotein protein particles catalyze the majority of pseudouridylation in functional RNA. Different from stand alone pseudouridine synthases, the RNP pseudouridine synthase comprises multiple protein subunits and an RNA subunit. Previous studies showed that each subunit, regardless its location, is sensitive to the step of subunit placement at the catalytic center and potentially to the reaction status of the substrate. Here we describe the impact of chemical substitutions of target uridine on enzyme activity and structure. We found that 3-methyluridine in place of uridine inhibited its isomerization while 2'-deoxyuridine or 4-thiouridine did not. Significantly, crystal structures of an archaeal box H/ACA RNP bound with the nonreactive and the two postreactive substrate analogues showed only subtle structural changes throughout the assembly except for a conserved tyrosine and a substrate anchoring loop of Cbf5. Our results suggest a potential role of these elements and the subunit that contacts them in substrate binding and product release.
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Affiliation(s)
- Jing Zhou
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306, USA
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Hamma T, Ferré-D'Amaré AR. The box H/ACA ribonucleoprotein complex: interplay of RNA and protein structures in post-transcriptional RNA modification. J Biol Chem 2009; 285:805-9. [PMID: 19917616 DOI: 10.1074/jbc.r109.076893] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The box H/ACA ribonucleoproteins (RNPs) are protein-RNA complexes responsible for pseudouridylation, the most abundant post-transcriptional modification of cellular RNAs. Integrity of its box H/ACA domain is also essential for assembly and stability of the human telomerase RNP. The recent publication of the complete box H/ACA RNP structures combined with the previously reported structures of the protein and RNA components makes it possible to deduce the structural accommodation that accompanies assembly of the full particle. This analysis reveals how the protein components distort the RNA component of the RNP, enabling productive docking of the substrate RNA into the enzymatic active site.
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Affiliation(s)
- Tomoko Hamma
- Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
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Alian A, DeGiovanni A, Griner SL, Finer-Moore JS, Stroud RM. Crystal structure of an RluF-RNA complex: a base-pair rearrangement is the key to selectivity of RluF for U2604 of the ribosome. J Mol Biol 2009; 388:785-800. [PMID: 19298824 DOI: 10.1016/j.jmb.2009.03.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 02/18/2009] [Accepted: 03/11/2009] [Indexed: 12/25/2022]
Abstract
Escherichia coli pseudouridine synthase RluF is dedicated to modifying U2604 in a stem-loop of 23S RNA, while a homologue, RluB, modifies the adjacent base, U2605. Both uridines are in the same RNA stem, separated by approximately 4 A. The 3.0 A X-ray crystal structure of RluF bound to the isolated stem-loop, in which U2604 is substituted by 5-fluorouridine to prevent catalytic turnover, shows RluF distinguishes closely spaced bases in similar environments by a selectivity mechanism based on a frameshift in base pairing. The RNA stem-loop is bound to a conserved binding groove in the catalytic domain. A base from a bulge in the stem, A2602, has folded into the stem, forcing one strand of the RNA stem to translate by one position and thus positioning U2604 to flip into the active site. RluF does not modify U2604 in mutant stem-loops that lack the A2602 bulge and shows dramatically higher activity for a stem-loop with a mutation designed to facilitate A2602 refolding into the stem with concomitant RNA strand translation. Residues whose side chains contact rearranged bases in the bound stem-loop, while conserved among RluFs, are not conserved between RluFs and RluBs, suggesting that RluB does not bind to the rearranged stem loop.
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Affiliation(s)
- Akram Alian
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158-2517, USA
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Ishitani R, Yokoyama S, Nureki O. Structure, dynamics, and function of RNA modification enzymes. Curr Opin Struct Biol 2008; 18:330-9. [DOI: 10.1016/j.sbi.2008.05.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2008] [Accepted: 05/04/2008] [Indexed: 01/20/2023]
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Matte A, Jia Z, Sunita S, Sivaraman J, Cygler M. Insights into the biology of Escherichia coli through structural proteomics. ACTA ACUST UNITED AC 2007; 8:45-55. [PMID: 17668295 DOI: 10.1007/s10969-007-9019-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Accepted: 06/28/2007] [Indexed: 10/23/2022]
Abstract
Escherichia coli has historically been an important organism for understanding a multitude of biological processes, and represents a model system as we attempt to simulate the workings of living cells. Many E. coli strains are also important human and animal pathogens for which new therapeutic strategies are required. For both reasons, a more complete and comprehensive understanding of the protein structure complement of E. coli is needed at the genome level. Here, we provide examples of insights into the mechanism and function of bacterial proteins that we have gained through the Bacterial Structural Genomics Initiative (BSGI), focused on medium-throughput structure determination of proteins from E. coli. We describe the structural characterization of several enzymes from the histidine biosynthetic pathway, the structures of three pseudouridine synthases, enzymes that synthesize one of the most abundant modified bases in RNA, as well as the combined use of protein structure and focused functional analysis to decipher functions for hypothetical proteins. Together, these results illustrate the power of structural genomics to contribute to a deeper biological understanding of bacterial processes.
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Affiliation(s)
- Allan Matte
- Biotechnology Research Institute, National Research Council Canada, Montreal, QC, Canada.
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