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Korobeinikova AV, Garber MB, Gongadze GM. Ribosomal proteins: structure, function, and evolution. BIOCHEMISTRY (MOSCOW) 2012; 77:562-74. [PMID: 22817455 DOI: 10.1134/s0006297912060028] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The question concerning reasons for the variety of ribosomal proteins that arose for more than 40 years ago is still open. Ribosomes of modern organisms contain 50-80 individual proteins. Some are characteristic for all domains of life (universal ribosomal proteins), whereas others are specific for bacteria, archaea, or eucaryotes. Extensive information about ribosomal proteins has been obtained since that time. However, the role of the majority of ribosomal proteins in the formation and functioning of the ribosome is still not so clear. Based on recent data of experiments and bioinformatics, this review presents a comprehensive evaluation of structural conservatism of ribosomal proteins from evolutionarily distant organisms. Considering the current knowledge about features of the structural organization of the universal proteins and their intermolecular contacts, a possible role of individual proteins and their structural elements in the formation and functioning of ribosomes is discussed. The structural and functional conservatism of the majority of proteins of this group suggests that they should be present in the ribosome already in the early stages of its evolution.
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Affiliation(s)
- A V Korobeinikova
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Moscow Region, Russia
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Lüer C, Schauer S, Virus S, Schubert WD, Heinz DW, Moser J, Jahn D. Glutamate recognition and hydride transfer by Escherichia coli glutamyl-tRNA reductase. FEBS J 2007; 274:4609-14. [PMID: 17697121 DOI: 10.1111/j.1742-4658.2007.05989.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The initial step of tetrapyrrole biosynthesis in Escherichia coli involves the NADPH-dependent reduction by glutamyl-tRNA reductase (GluTR) of tRNA-bound glutamate to glutamate-1-semialdehyde. We evaluated the contribution of the glutamate moiety of glutamyl-tRNA to substrate specificity in vitro using a range of substrates and enzyme variants. Unexpectedly, we found that tRNA(Glu) mischarged with glutamine was a substrate for purified recombinant GluTR. Similarly unexpectedly, the substitution of amino acid residues involved in glutamate side chain binding (S109A, T49V, R52K) or in stabilizing the arginine 52 glutamate interaction (glutamate 54 and histidine 99) did not abrogate enzyme activity. Replacing glutamine 116 and glutamate 114, involved in glutamate-enzyme interaction near the aminoacyl bond to tRNA(Glu), by leucine and lysine, respectively, however, did abolish reductase activity. We thus propose that the ester bond between glutamate and tRNA(Glu) represents the crucial determinant for substrate recognition by GluTR, whereas the necessity for product release by a 'back door' exit allows for a degree of structural variability in the recognition of the amino acid moiety. Analyzing the esterase activity, which occured in the absence of NADPH, of GluTR variants using the substrate 4-nitrophenyl acetate confirmed the crucial role of cysteine 50 for thioester formation. Finally, the GluTR variant Q116L was observed to lack reductase activity whereas esterase activity was retained. Structure-based molecular modeling indicated that glutamine 116 may be crucial in positioning the nicotinamide group of NADPH to allow for productive hydride transfer to the substrate. Our data thus provide new information about the distinct function of active site residues of GluTR from E. coli.
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Affiliation(s)
- Corinna Lüer
- Institute of Microbiology, Technical University Braunschweig, Germany
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Unique features of selenocysteine incorporation function within the context of general eukaryotic translational processes. Biochem Soc Trans 2005; 33:1493-7. [PMID: 16246153 DOI: 10.1042/bst0331493] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Unlike other essential dietary trace elements, selenium exerts its biological actions through its direct incorporation into selenoproteins, as a part of the 21st amino acid, selenocysteine. Fundamental studies have elucidated the unique structures and putative functions of multiple co-translational factors required for the incorporation of selenocysteine into selenoproteins. The current challenge is to understand how these selenocysteine incorporation factors function within the framework of translation. In eukaryotes, co-ordinating nuclear transcription with cytoplasmic translation of genes is a challenge involving complex spatial and temporal regulation. Selenoproteins utilize the common cellular machinery required for synthesis of non-selenoproteins. This machinery includes the elements involved in transcription, mRNA splicing and transport, and translational processes. Many investigators have emphasized the differences between the expression of selenoproteins and other eukaryotic proteins, whereas this review will attempt to highlight common themes and point out where additional interactions may be discovered.
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Abstract
The exit tunnel region of the ribosome is well established as a focal point for interaction between the components that guide the fate of nascent polypeptides. One of these, the chaperone trigger factor (TF), associates with the 50S ribosomal subunit through its N-terminal domain. Targeting of TF to ribosomes is crucial to achieve its remarkable efficiency in protein folding. A similar tight coupling to translation is found in signal recognition particle (SRP)-dependent protein translocation. Here, we report crystal structures of the E. coli TF ribosome binding domain. TF is structurally related to the Hsp33 chaperone but has a prominent ribosome anchor located as a tip of the molecule. This tip includes the previously established unique TF signature motif. Comparison reveals that this feature is not found in SRP structures. We identify a conserved helical kink as a hallmark of the TF structure that is most likely critical to ensure ribosome association.
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Affiliation(s)
- Ole Kristensen
- Structural Biology, Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen, Denmark.
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Cox RA. Correlation of the rate of protein synthesis and the third power of the RNA : protein ratio in Escherichia coli and Mycobacterium tuberculosis. MICROBIOLOGY (READING, ENGLAND) 2003; 149:729-737. [PMID: 12634341 DOI: 10.1099/mic.0.25645-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In order to further understand the different physiological states of the tubercle bacillus, a frame of reference was sought by first correlating the macromolecular compositions of Escherichia coli with specific growth rates and also with the rates of protein synthesis. Data for DNA : protein : RNA were converted to the average amounts of DNA [m(DNA(av))], protein [m(p(av))] and RNA [m(RNA(av))] per cell. The specific growth rate micro was found to be directly proportional to m(RNA(av))/m(p(av)). The specific protein synthesis rate per average cell [omega(p(av))] was shown to be directly proportional to the third power of the ratio m(RNA(av))/m(p(av)) which reflects the ribosome concentration. The equations derived were shown apply to both E. coli ( micro =1.73 h(-1)) and Mycobacterium bovis BCG ( micro =0.029 h(-1)).
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Affiliation(s)
- Robert A Cox
- Division of Mycobacterial Research, National Institute for Medical Research, London NW7 1AA, UK
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Moser J, Schubert WD, Beier V, Bringemeier I, Jahn D, Heinz DW. V-shaped structure of glutamyl-tRNA reductase, the first enzyme of tRNA-dependent tetrapyrrole biosynthesis. EMBO J 2001; 20:6583-90. [PMID: 11726494 PMCID: PMC125327 DOI: 10.1093/emboj/20.23.6583] [Citation(s) in RCA: 89] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Processes vital to life such as respiration and photosynthesis critically depend on the availability of tetrapyrroles including hemes and chlorophylls. tRNA-dependent catalysis generally is associated with protein biosynthesis. An exception is the reduction of glutamyl-tRNA to glutamate-1-semialdehyde by the enzyme glutamyl-tRNA reductase. This reaction is the indispensable initiating step of tetrapyrrole biosynthesis in plants and most prokaryotes. The crystal structure of glutamyl-tRNA reductase from the archaeon Methanopyrus kandleri in complex with the substrate-like inhibitor glutamycin at 1.9 A resolution reveals an extended yet planar V-shaped dimer. The well defined interactions of the inhibitor with the active site support a thioester-mediated reduction process. Modeling the glutamyl-tRNA onto each monomer reveals an extensive protein-tRNA interface. We furthermore propose a model whereby the large void of glutamyl-tRNA reductase is occupied by glutamate-1-semialdehyde-1,2-mutase, the subsequent enzyme of this pathway, allowing for the efficient synthesis of 5-aminolevulinic acid, the common precursor of all tetrapyrroles.
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Affiliation(s)
| | - Wolf-Dieter Schubert
- Institute of Microbiology, Technical University Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig,
Department of Structural Biology, German Research Center for Biotechnology, Mascheroder Weg 1, D-38104 Braunschweig and Microsoft Germany Inc., Germany Corresponding author e-mail: J.Moser and W.D.Schubert contributed equally to this work
| | - Viola Beier
- Institute of Microbiology, Technical University Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig,
Department of Structural Biology, German Research Center for Biotechnology, Mascheroder Weg 1, D-38104 Braunschweig and Microsoft Germany Inc., Germany Corresponding author e-mail: J.Moser and W.D.Schubert contributed equally to this work
| | - Ingo Bringemeier
- Institute of Microbiology, Technical University Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig,
Department of Structural Biology, German Research Center for Biotechnology, Mascheroder Weg 1, D-38104 Braunschweig and Microsoft Germany Inc., Germany Corresponding author e-mail: J.Moser and W.D.Schubert contributed equally to this work
| | | | - Dirk W. Heinz
- Institute of Microbiology, Technical University Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig,
Department of Structural Biology, German Research Center for Biotechnology, Mascheroder Weg 1, D-38104 Braunschweig and Microsoft Germany Inc., Germany Corresponding author e-mail: J.Moser and W.D.Schubert contributed equally to this work
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Vitagliano L, Masullo M, Sica F, Zagari A, Bocchini V. The crystal structure of Sulfolobus solfataricus elongation factor 1alpha in complex with GDP reveals novel features in nucleotide binding and exchange. EMBO J 2001; 20:5305-11. [PMID: 11574461 PMCID: PMC125647 DOI: 10.1093/emboj/20.19.5305] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The crystal structure of elongation factor 1alpha from the archaeon Sulfolobus solfataricus in complex with GDP (SsEF-1alpha.GDP) at 1.8 A resolution is reported. As already known for the eubacterial elongation factor Tu, the SsEF-1alpha.GDP structure consists of three different structural domains. Surprisingly, the analysis of the GDP-binding site reveals that the nucleotide- protein interactions are not mediated by Mg(2+). Furthermore, the residues that usually co-ordinate Mg(2+) through water molecules in the GTP-binding proteins, though conserved in SsEF-1alpha, are located quite far from the binding site. [(3)H]GDP binding experiments confirm that Mg(2+) has only a marginal effect on the nucleotide exchange reaction of SsEF-1alpha, although essential to GTPase activity elicited by SsEF-1alpha. Finally, structural comparisons of SsEF- 1alpha.GDP with yeast EF-1alpha in complex with the nucleotide exchange factor EF-1beta shows that a dramatic rearrangement of the overall structure of EF-1alpha occurs during the nucleotide exchange.
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Affiliation(s)
- Luigi Vitagliano
- Centro di Biocristallografia, CNR, via Mezzocannone 6, I-80134 Napoli, Dipartimento di Biochimica e Biotecnologie Mediche Via Pansini 5, I-80131 Napoli and Dipartimento di Chimica, Università degli studi di Napoli ‘Federico II’, Dipartimento di Scienze Farmacobiologiche, Università degli Studi di Catanzaro ‘Magna Graecia’, Catanzaro and CEINGE, Biotecnologie avanzate Scarl, Napoli, Italy Corresponding author e-mail: Deceased June 28, 2001
| | - Mariorosario Masullo
- Centro di Biocristallografia, CNR, via Mezzocannone 6, I-80134 Napoli, Dipartimento di Biochimica e Biotecnologie Mediche Via Pansini 5, I-80131 Napoli and Dipartimento di Chimica, Università degli studi di Napoli ‘Federico II’, Dipartimento di Scienze Farmacobiologiche, Università degli Studi di Catanzaro ‘Magna Graecia’, Catanzaro and CEINGE, Biotecnologie avanzate Scarl, Napoli, Italy Corresponding author e-mail: Deceased June 28, 2001
| | - Filomena Sica
- Centro di Biocristallografia, CNR, via Mezzocannone 6, I-80134 Napoli, Dipartimento di Biochimica e Biotecnologie Mediche Via Pansini 5, I-80131 Napoli and Dipartimento di Chimica, Università degli studi di Napoli ‘Federico II’, Dipartimento di Scienze Farmacobiologiche, Università degli Studi di Catanzaro ‘Magna Graecia’, Catanzaro and CEINGE, Biotecnologie avanzate Scarl, Napoli, Italy Corresponding author e-mail: Deceased June 28, 2001
| | - Adriana Zagari
- Centro di Biocristallografia, CNR, via Mezzocannone 6, I-80134 Napoli, Dipartimento di Biochimica e Biotecnologie Mediche Via Pansini 5, I-80131 Napoli and Dipartimento di Chimica, Università degli studi di Napoli ‘Federico II’, Dipartimento di Scienze Farmacobiologiche, Università degli Studi di Catanzaro ‘Magna Graecia’, Catanzaro and CEINGE, Biotecnologie avanzate Scarl, Napoli, Italy Corresponding author e-mail: Deceased June 28, 2001
| | - Vincenzo Bocchini
- Centro di Biocristallografia, CNR, via Mezzocannone 6, I-80134 Napoli, Dipartimento di Biochimica e Biotecnologie Mediche Via Pansini 5, I-80131 Napoli and Dipartimento di Chimica, Università degli studi di Napoli ‘Federico II’, Dipartimento di Scienze Farmacobiologiche, Università degli Studi di Catanzaro ‘Magna Graecia’, Catanzaro and CEINGE, Biotecnologie avanzate Scarl, Napoli, Italy Corresponding author e-mail: Deceased June 28, 2001
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Abstract
The role of tRNA as the adaptor in protein synthesis has held an enduring fascination for molecular biologists. Over four decades of study, taking in numerous milestones in molecular biology, led to what was widely held to be a fairly complete picture of how tRNAs and amino acids are paired prior to protein synthesis. However, recent developments in genomics and structural biology have revealed an unexpected array of new enzymes, pathways and mechanisms involved in aminoacyl-tRNA synthesis. As a more complete picture of aminoacyl-tRNA synthesis now begins to emerge, the high degree of evolutionary diversity in this universal and essential process is becoming clearer.
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Affiliation(s)
- M Ibba
- Center for Biomolecular Recognition, Department of Medical Biochemistry and Genetics, Laboratory B, The Panum Institute, Blegdamsvej 3c, DK-2200, Copenhagen N,
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Kuthan H. Self-organisation and orderly processes by individual protein complexes in the bacterial cell. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2001; 75:1-17. [PMID: 11311713 DOI: 10.1016/s0079-6107(00)00023-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
In the bacterial cell, individual multimeric proteins and multiprotein assemblies perform and control orderly processes. Individual motor enzyme complexes accomplish highly complex functions, such as nucleic acid and protein syntheses, with impressive efficiency and fidelity. Lac operon repression by the lac repressor is effectively controlled via a single molecular switch. There are only few copies of, for example, DNA polymerase holoenzyme and lac repressor and few specific target molecules/sites, with which these protein complexes interact, present in a single E. coli cell. These interactive processes take place in submicron-sized spaces characterised by extreme crowding (volume exclusion) of macromolecules and small molecules, heterogeneity and non-ideality. Recent evidence reinforces the fundamental difference of the cytoplasmic as compared with in vitro ("test tube") reaction conditions. This is reflected in the breakdown of the applicability of "bulk phase" thermodynamic, macroscopic chemical kinetic and diffusion laws to interactions of individual macromolecules and target sites in a single cell. Stochastic kinetic models and stochastic simulations enable the statistical description and analysis of biochemical reactions and binding processes which involve small numbers of reactants. New unifying concepts and models are required for the quantitative understanding of the microscopic self-organisation of multi-protein complexes and the dynamic order at the single-protein assembly and single-switch level in the living cell.
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