1
|
Goodfellow BJ, Freire F, Carvalho AL, Aveiro SS, Charbonnier P, Moulis JM, Delgado L, Ferreira GC, Rodrigues JE, Poussin-Courmontagne P, Birck C, McEwen A, Macedo AL. The SOUL family of heme-binding proteins: Structure and function 15 years later. Coord Chem Rev 2021. [DOI: 10.1016/j.ccr.2021.214189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
|
2
|
Kasireddy C, Ellis JM, Bann JG, Mitchell-Koch KR. Tautomeric stabilities of 4-fluorohistidine shed new light on mechanistic experiments with labeled ribonuclease A. Chem Phys Lett 2016; 666:58-61. [PMID: 28603294 DOI: 10.1016/j.cplett.2016.10.072] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Ribonuclease A is the oldest model for studying enzymatic mechanisms, yet questions remain about proton transfer within the active site. Seminal work by Jackson et al. (Science, 1994) labeled Ribonuclease A with 4-fluorohistidine, concluding that active-site histidines act as general acids and bases. Calculations of 4-fluorohistidine indicate that the π-tautomer is predominant in all simulated environments (by ~17 kJ/mol), strongly suggesting that fluoro-labeled ribonuclease A functions with His119 in π-tautomer. The tautomeric form of His119 during proton transfer and tautomerism as a putative mechanistic step in wild-type RNase A remain open questions and should be considered in future mechanistic studies.
Collapse
Affiliation(s)
- Chandana Kasireddy
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, United States
| | - Jonathan M Ellis
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, United States
| | - James G Bann
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, United States
| | - Katie R Mitchell-Koch
- Department of Chemistry, Wichita State University, 1845 Fairmount Street, Wichita, KS 67260-0051, United States
| |
Collapse
|
3
|
Plantinga MJ, Korennykh AV, Piccirilli JA, Correll CC. The ribotoxin restrictocin recognizes its RNA substrate by selective engagement of active site residues. Biochemistry 2011; 50:3004-13. [PMID: 21417210 PMCID: PMC3071035 DOI: 10.1021/bi1018336] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
![]()
Restrictocin and related fungal endoribonucleases from the α-sarcin family site-specifically cleave the sarcin/ricin loop (SRL) on the ribosome to inhibit translation and ultimately trigger cell death. Previous studies showed that the SRL folds into a bulged-G motif and tetraloop, with restrictocin achieving a specificity of ∼1000-fold by recognizing both motifs only after the initial binding step. Here, we identify contacts within the protein−RNA interface and determine the extent to which each one contributes to enzyme specificity by examining the effect of protein mutations on the cleavage of the SRL substrate compared to a variety of other RNA substrates. As with other biomolecular interfaces, only a subset of contacts contributes to specificity. One contact of this subset is critical, with the H49A mutation resulting in quantitative loss of specificity. Maximum catalytic activity occurs when both motifs of the SRL are present, with the major contribution involving the bulged-G motif recognized by three lysine residues located adjacent to the active site: K110, K111, and K113. Our findings support a kinetic proofreading mechanism in which the active site residues H49 and, to a lesser extent, Y47 make greater catalytic contributions to SRL cleavage than to suboptimal substrates. This systematic and quantitative analysis begins to elucidate the principles governing RNA recognition by a site-specific endonuclease and may thus serve as a mechanistic model for investigating other RNA modifying enzymes.
Collapse
Affiliation(s)
- Matthew J Plantinga
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois 60637, USA
| | | | | | | |
Collapse
|
4
|
Hass MAS, Yilmaz A, Christensen HEM, Led JJ. Histidine side-chain dynamics and protonation monitored by 13C CPMG NMR relaxation dispersion. JOURNAL OF BIOMOLECULAR NMR 2009; 44:225-233. [PMID: 19533375 DOI: 10.1007/s10858-009-9332-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Accepted: 05/28/2009] [Indexed: 05/27/2023]
Abstract
The use of 13C NMR relaxation dispersion experiments to monitor micro-millisecond fluctuations in the protonation states of histidine residues in proteins is investigated. To illustrate the approach, measurements on three specifically 13C labeled histidine residues in plastocyanin (PCu) from Anabaena variabilis (A.v.) are presented. Significant Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion is observed for 13C(epsilon1) nuclei in the histidine imidazole rings of A.v. PCu. The chemical shift changes obtained from the CPMG dispersion data are in good agreement with those obtained from the chemical shift titration experiments, and the CPMG derived exchange rates agree with those obtained previously from 15N backbone relaxation measurements. Compared to measurements of backbone nuclei, 13C(epsilon1) dispersion provides a more direct method to monitor interchanging protonation states or other kinds of conformational changes of histidine side chains or their environment. Advantages and shortcomings of using the 13C(epsilon1) dispersion experiments in combination with chemical shift titration experiments to obtain information on exchange dynamics of the histidine side chains are discussed.
Collapse
Affiliation(s)
- Mathias A S Hass
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen Ø, Denmark
| | | | | | | |
Collapse
|
5
|
Hass MAS, Hansen DF, Christensen HEM, Led JJ, Kay LE. Characterization of Conformational Exchange of a Histidine Side Chain: Protonation, Rotamerization, and Tautomerization of His61 in Plastocyanin from Anabaena variabilis. J Am Chem Soc 2008; 130:8460-70. [DOI: 10.1021/ja801330h] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mathias A. S. Hass
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, and Department of Chemistry, The Technical University of Denmark, 2800 Lyngby, Denmark
| | - D. Flemming Hansen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, and Department of Chemistry, The Technical University of Denmark, 2800 Lyngby, Denmark
| | - Hans E. M. Christensen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, and Department of Chemistry, The Technical University of Denmark, 2800 Lyngby, Denmark
| | - Jens J. Led
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, and Department of Chemistry, The Technical University of Denmark, 2800 Lyngby, Denmark
| | - Lewis E. Kay
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, Departments of Molecular Genetics, Biochemistry, and Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8, and Department of Chemistry, The Technical University of Denmark, 2800 Lyngby, Denmark
| |
Collapse
|
6
|
Lacadena J, Alvarez-García E, Carreras-Sangrà N, Herrero-Galán E, Alegre-Cebollada J, García-Ortega L, Oñaderra M, Gavilanes JG, Martínez del Pozo A. Fungal ribotoxins: molecular dissection of a family of natural killers. FEMS Microbiol Rev 2007; 31:212-37. [PMID: 17253975 DOI: 10.1111/j.1574-6976.2006.00063.x] [Citation(s) in RCA: 109] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
RNase T1 is the best known representative of a large family of ribonucleolytic proteins secreted by fungi, mostly Aspergillus and Penicillium species. Ribotoxins stand out among them by their cytotoxic character. They exert their toxic action by first entering the cells and then cleaving a single phosphodiester bond located within a universally conserved sequence of the large rRNA gene, known as the sarcin-ricin loop. This cleavage leads to inhibition of protein biosynthesis, followed by cellular death by apoptosis. Although no protein receptor has been found for ribotoxins, they preferentially kill cells showing altered membrane permeability, such as those that are infected with virus or transformed. Many steps of the cytotoxic process have been elucidated at the molecular level by means of a variety of methodological approaches and the construction and purification of different mutant versions of these ribotoxins. Ribotoxins have been used for the construction of immunotoxins, because of their cytotoxicity. Besides this activity, Aspf1, a ribotoxin produced by Aspergillus fumigatus, has been shown to be one of the major allergens involved in allergic aspergillosis-related pathologies. Protein engineering and peptide synthesis have been used in order to understand the basis of these pathogenic mechanisms as well as to produce hypoallergenic proteins with potential diagnostic and immunotherapeutic applications.
Collapse
Affiliation(s)
- Javier Lacadena
- Departamento de Bioquímica y Biología Molecular I, Facultad de Química, Universidad Complutense, 28040 Madrid, Spain
| | | | | | | | | | | | | | | | | |
Collapse
|
7
|
García-Mayoral MF, Pérez-Cañadillas JM, Santoro J, Ibarra-Molero B, Sanchez-Ruiz JM, Lacadena J, Martínez del Pozo A, Gavilanes JG, Rico M, Bruix M. Dissecting Structural and Electrostatic Interactions of Charged Groups in α-Sarcin. An NMR Study of Some Mutants Involving the Catalytic Residues. Biochemistry 2003; 42:13122-33. [PMID: 14609322 DOI: 10.1021/bi0349773] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cytotoxic ribonuclease alpha-sarcin is the best characterized member of the ribotoxin family. Ribotoxins share a common structural core, catalytic residues, and active site topology with members of the broader family of nontoxic microbial extracellular RNases. They are, however, much more specific in their biological action. To shed light on the highly specific alpha-sarcin activity, we have evaluated the structural and electrostatic interactions of its charged groups, by combining the structural and pK(a) characterization by NMR of several variants with theoretical calculations based on the Tanford-Kirkwood and Poisson-Boltzmann models. The NMR data reveal that the global conformation of wild-type alpha-sarcin is preserved in the H50Q, E96Q, H137Q, and H50/137Q variants, and that His137 is involved in an H-bond that is crucial in maintaining the active site structure and in reinforcing the stability of the enzyme. The loss of this H-bond in the H137Q and H50/137Q variants modifies the local structure of the active site. The pK(a) values of active site groups H50, E96, and H137 in the four variants have been determined by two-dimensional NMR. The catalytic dyad of E96 and H137 is not sensitive to charge replacements, since their pK(a) values vary less than +/-0.3 pH unit with respect to those of the wild type. On the contrary, the pK(a) of His50 undergoes drastic changes when compared to its value in the intact protein. These amount to an increase of 0.5 pH unit or a decrease of 1.1 pH units depending on whether a positive or negative charge is substituted at the active site. The main determinants of the pK(a) values of most of the charged groups in alpha-sarcin have been established by considering the NMR results in conjunction with those derived from theoretical pK(a) calculations. With regard to the active site residues, the H50 pK(a) is chiefly influenced by electrostatic interactions with E96 and H137, whereas the effect of the low dielectric constant and the interaction with R121 appear to be the main determinants of the altered pK(a) value of E96 and H137. Charge-charge interactions and an increased level of burial perturb the pK(a) values of the active site residues of alpha-sarcin, which can account for its reduced ribonucleolytic activity and its high specificity.
Collapse
Affiliation(s)
- Ma Flor García-Mayoral
- Departamento de Espectroscopía y Estructura Molecular, Instituto de Química Física Rocasolano, CSIC, Serrano 119, 28006 Madrid, Spain
| | | | | | | | | | | | | | | | | | | |
Collapse
|