201
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Sekiguchi J, Shuman S. Covalent DNA binding by vaccinia topoisomerase results in unpairing of the thymine base 5' of the scissile bond. J Biol Chem 1996; 271:19436-42. [PMID: 8702632 DOI: 10.1074/jbc.271.32.19436] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
We have used potassium permanganate to probe contacts between vaccinia DNA topoisomerase and thymine residues in its 5'-CCCTT downward arrow DNA target site. Two major conclusions emerge from the experiments presented: (i) permanganate oxidation of the +2T base of the scissile strand interferes with topoisomerase binding to DNA, and (ii) the +1T base of the scissile strand becomes unpaired upon formation of the covalent topoisomerase-DNA intermediate. Disruption of T:A base pairing is confined to the +1-position. Covalently bound DNAs that have experienced this structural distortion (such DNAs being marked by oxidation at +1T) are fully capable of being religated. We suggest that a protein-induced DNA conformational change is a component of the strand passage step of the topoisomerase reaction.
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Affiliation(s)
- J Sekiguchi
- Molecular Biology Program, Sloan-Kettering Institute, New York, New York 10021, USA
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202
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Ceska TA, Sayers JR, Stier G, Suck D. A helical arch allowing single-stranded DNA to thread through T5 5'-exonuclease. Nature 1996; 382:90-3. [PMID: 8657312 DOI: 10.1038/382090a0] [Citation(s) in RCA: 158] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
THE 5'-exonucleases are enzymes that are essential for DNA replication and repair. As well as their exonucleolytic action, removing nucleotides from the 5'-end of nucleic acid molecules such as Okazaki fragments, many 5'-3'-exonucleases have been shown to possess endonucleolytic activities. T5 5'-3'-exonuclease shares many similarities with the amino terminal of eubacterial DNA polymerases, although, unlike eubacteria, phages such as T5, T4 and T7 express polymerase and 5'-exonuclease proteins from separate genes. Here we report the 2.5-A crystal structure of the phage T5 5'-exonuclease, which reveals a helical arch for binding DNA. We propose a model consistent with a threading mechanism in which single-stranded DNA could slide through the arch, which is formed by two helices, one containing positively charged, and the other hydrophobic, residues. The active site is at the base of the arch, and contains two metal-binding sites.
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Affiliation(s)
- T A Ceska
- EMBL, Structural Biology Programme, Heidelberg, Germany.
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203
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Alami-Ouahabi N, Veilleux S, Meistrich ML, Boissonneault G. The testis-specific high-mobility-group protein, a phosphorylation-dependent DNA-packaging factor of elongating and condensing spermatids. Mol Cell Biol 1996; 16:3720-9. [PMID: 8668189 PMCID: PMC231368 DOI: 10.1128/mcb.16.7.3720] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Mammalian spermiogenesis is characterized by a striking restructuring of the spermatid chromatin caused by the replacement of nucleohistones with transition proteins and their subsequent replacement with nucleoprotamines. The onset of nuclear elongation and chromatin condensation in spermatids is accompanied by a general decrease in the transcriptional activity of the DNA. A recently identified testis-specific high-mobility-group (tsHMG) protein, similar to the human mitochondrial transcription factor I and to the linker-associated protein delta of Tetrahymena thermophila micronuclei, is thought to play a structural role in this process. We confirm by immunoblot analysis of fractionated germ cells that the presence of tsHMG is restricted to transcriptionally quiescent elongating and condensing spermatids. Purified recombinant tsHMG protein displays preferential binding to supercoiled plasmid DNA, which reversibly protects the DNA against the DNA-relaxing activity of eukaryotic topoisomerase I and also impairs the transcriptional activity of this template when assayed in vitro. The tsHMG protein can also introduce negative supercoils into a relaxed plasmid substrate in a topoisomerase I-dependent manner. We also show that the tsHMG protein is the substrate of a Ca2+-phospholipid-dependent protein kinase (protein kinase C) present in testis extracts of adult mice and demonstrate that phosphorylation by protein kinase C is required for both the DNA-binding and the topoisomerase I-dependent supercoiling activities of tsHMG. Our results support the hypothesis that the spermatid tsHMG protein is a topological factor (transition protein) that can modulate the activity of topoisomerase I. This activity could contribute to the important transition in chromatin structure which leads to the decrease in DNA metabolism observed at the early stages of spermatid elongation.
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Affiliation(s)
- N Alami-Ouahabi
- Department of Biochemistry, Faculty of Medicine, University of Sherbrooke, Quebec, Canada
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204
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Shimamoto T, Imajo S, Honda T, Yoshimura S, Ishiguro M. Structure-activity relationship study on N-glycosyl moieties through model building of DNA and ellipticine N-glycoside complex. Bioorg Med Chem Lett 1996. [DOI: 10.1016/0960-894x(96)00219-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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205
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Zhang HL, Malpure S, Li Z, Hiasa H, DiGate RJ. The role of the carboxyl-terminal amino acid residues in Escherichia coli DNA topoisomerase III-mediated catalysis. J Biol Chem 1996; 271:9039-45. [PMID: 8621552 DOI: 10.1074/jbc.271.15.9039] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
The role that the carboxyl-terminal amino acids of Escherichia coli DNA topoisomerase I (Topo I) and III (Topo III) play in catalysis was examined by comparing the properties of Topo III with those of a truncated enzyme lacking the generalized DNA binding domain of Topo III, Topo I, and a hybrid topoisomerase polypeptide containing the amino-terminal 605 amino acids of Topo III and the putative generalized DNA binding domain of Topo I. The deletion of the carboxyl-terminal 49 amino acids of Topo III decreases the affinity of the enzyme for its substrate, single-stranded DNA, by approximately 2 orders of magnitude and reduces Topo III-catalyzed relaxation of supercoiled DNA and Topo III-catalyzed resolution of DNA replication intermediates to a similar extent. Fusion of the carboxyl-terminal 312 amino acid residues of Topo I onto the truncated molecule stimulates topoisomerase-catalyzed relaxation 15-20-fold, to a level comparable with that of full-length Topo III. However, topoisomerase-catalyzed resolution of DNA replication intermediates was only stimulated 2-3-fold. Therefore, the carboxyl-terminal amino acids of these topoisomerases constitute a distinct and separable domain, and this domain is intimately involved in determining the catalytic properties of these polypeptides.
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Affiliation(s)
- H L Zhang
- Molecular and Cell Biology Program, University of Maryland, Baltimore, Maryland 21201, USA
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206
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207
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Abstract
The crystal structure of a large fragment of yeast type II DNA topoisomerase reveals a heart-shaped dimeric protein with a large central hole. It provides a molecular model of the enzyme as an ATP-modulated clamp with two sets of jaws at opposite ends, connected by multiple joints. An enzyme with bound DNA can admit a second DNA duplex through one set of jaws, transport it through the cleaved first duplex, and expel it through the other set of jaws.
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Affiliation(s)
- J M Berger
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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208
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Krah R, Kozyavkin SA, Slesarev AI, Gellert M. A two-subunit type I DNA topoisomerase (reverse gyrase) from an extreme hyperthermophile. Proc Natl Acad Sci U S A 1996; 93:106-10. [PMID: 8552584 PMCID: PMC40187 DOI: 10.1073/pnas.93.1.106] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
A recently described reverse gyrase from the hyperthermophilic methanogen Methanopyrus kandleri is the only known example of a heterodimeric type I topoisomerase. The enzyme is made up of a 42-kDa subunit which covalently interacts with DNA (RgyA) and a 138-kDa subunit which binds ATP (RgyB). We have now cloned and sequenced the genes for both subunits of this enzyme. Surprisingly, the universally conserved type I topoisomerase domain [Lima, C. D., Wang, J. C. & Mondragon, A. (1994) Nature (London) 367, 138-146] which has been found as a contiguous polypeptide in the prokaryotes and eukaryotes is shared between the protomers. The subdomain with the active-site tyrosine is entirely within RgyA, whereas the subdomain implicated in noncovalent binding of the cleaved DNA strand is contained entirely in RgyB. The appearance of this unique structure in a highly conserved enzyme family supports the hypothesis that the methanogens branched from other prokaryotes and eukaryotes very early in evolution.
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Affiliation(s)
- R Krah
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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209
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210
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Curran DP, Ko SB, Josien H. Kaskaden-Radikalreaktionen von Isocyaniden: eine zweite Generation der Synthese von (20S)-Camptothecin, Topotecan, Irinotecan und GI-147211C. Angew Chem Int Ed Engl 1995. [DOI: 10.1002/ange.19951072344] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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211
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Lue N, Sharma A, Mondragón A, Wang JC. A 26 kDa yeast DNA topoisomerase I fragment: crystallographic structure and mechanistic implications. Structure 1995; 3:1315-22. [PMID: 8747458 DOI: 10.1016/s0969-2126(01)00269-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
BACKGROUND Type I DNA topoisomerases, divided mechanistically into two subfamilies, are ubiquitous enzymes that participate in replication and transcription. In addition to its role in these fundamental processes, the biological importance of eukaryotic DNA topoisomerase I is underscored by its identification as the target of the antitumor alkaloid camptothecin. An understanding of the mechanism of catalysis and interactions with camptothecin and other drugs has been hampered by a lack of detailed structural information. RESULTS The three-dimensional structure of a 26 kDA fragment (residues 135 to about 363) of Saccharomyces cerevisiae DNA topoisomerase I has been determined at 1.9 A resolution. The fragment has a novel architecture comprising a concave platform and a pair of outlying V-shaped helices. Photocrosslinking and protein footprinting experiments show that the positively charged concave surface and the junction region of the V-shaped pair of helices contact DNA in the enzyme-DNA complex. CONCLUSIONS Crystallographic, biochemical and genetic data indicate that this 26 kDa fragment of yeast DNA topoisomerase I is involved in complex formation between the enzyme and DNA, and probably also in camptothecin-enzyme-DNA ternary complex formation. A molecular model for protein-DNA interaction based on these data is proposed. The bipartite DNA-binding regions of the 26 kDa fragment may enable eukaryotic DNA topoisomerase I to adapt to sequence-dependent structural variations in its DNA substrates.
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Affiliation(s)
- N Lue
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
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212
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Safro M, Mosyak L. Structural similarities in the noncatalytic domains of phenylalanyl-tRNA and biotin synthetases. Protein Sci 1995; 4:2429-32. [PMID: 8563641 PMCID: PMC2143022 DOI: 10.1002/pro.5560041122] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Detailed comparison between the structures of the Escherichia coli biotin synthetase/repressor protein (BirA) and the recently solved Thermus thermophilus phenylalanyl-tRNA synthetase (PheRS) reveals significant similarities outside their respective catalytic domains. These comprise a DNA-binding alpha+beta domain and an Src-homology 3 (SH3)-like domain that were observed in both enzymes. This similarity provides a novel example in which all domains of one multidomain protein appear to be constituents of the other multidomain protein and supports a concept of a common ancestor for two different synthetase families.
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Affiliation(s)
- M Safro
- Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
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213
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Abstract
Why do proteins proteins that encircle DNA have six-fold symmetry? One important factor may be the economy in protein mass with which DNA can be encircled by six globular subunits arranged in a ring.
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Affiliation(s)
- Z Kelman
- Microbiology Department, Hearst Research Foundation, Cornell University Medical College, New York, New York 10021, USA
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214
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Joshua-Tor L, Xu HE, Johnston SA, Rees DC. Crystal structure of a conserved protease that binds DNA: the bleomycin hydrolase, Gal6. Science 1995; 269:945-50. [PMID: 7638617 DOI: 10.1126/science.7638617] [Citation(s) in RCA: 106] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Bleomycin hydrolase is a cysteine protease that hydrolyzes the anticancer drug bleomycin. The homolog in yeast, Gal6, has recently been identified and found to bind DNA and to act as a repressor in the Gal4 regulatory system. The crystal structure of Gal6 at 2.2 A resolution reveals a hexameric structure with a prominent central channel. The papain-like active sites are situated within the central channel, in a manner resembling the organization of active sites in the proteasome. The Gal6 channel is lined with 60 lysine residues from the six subunits, suggesting a role in DNA binding. The carboxyl-terminal arm of Gal6 extends into the active site cleft and may serve a regulatory function. Rather than each residing in distinct, separable domains, the protease and DNA-binding activities appear structurally intertwined in the hexamer, implying a coupling of these two activities.
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Affiliation(s)
- L Joshua-Tor
- Divison of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125, USA
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215
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Naktinis V, Onrust R, Fang L, O'Donnell M. Assembly of a Chromosomal Replication Machine: Two DNA Polymerases, a Clamp Loader, and Sliding Clamps in One Holoenzyme Particle. J Biol Chem 1995. [DOI: 10.1074/jbc.270.22.13358] [Citation(s) in RCA: 120] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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216
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217
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Antson AA, Otridge J, Brzozowski AM, Dodson EJ, Dodson GG, Wilson KS, Smith TM, Yang M, Kurecki T, Gollnick P. The structure of trp RNA-binding attenuation protein. Nature 1995; 374:693-700. [PMID: 7715723 DOI: 10.1038/374693a0] [Citation(s) in RCA: 171] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The crystal structure of the trp RNA-binding attenuation protein of Bacclius subtilis solved at 1.8 A resolution reveals a novel structural arrangement in which the eleven subunits are stabilized through eleven intersubunit beta-sheets to form a beta-wheel with a large central hole. The nature of the binding of L-tryptophan in clefts between adjacent beta-sheets in the beta-wheel suggests that this binding induces conformational changes in the flexible residues 25-33 and 49-52. It is argued that upon binding, the messenger RNA target forms a matching circle in which eleven U/GAG repeats are bound to the surface of the protein ondecamer modified by the binding of L-tryptophan.
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Affiliation(s)
- A A Antson
- Department of Chemistry, University of York, UK
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218
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Abstract
DNA topoisomerases are essential to the cell for the regulation of DNA supercoiling levels and for chromosome decatenation. The proposed mechanisms for these reactions are essentially the same, except that a change in supercoiling is due to an intramolecular event, while decatenation requires an intermolecular event. The characterized bacterial topoisomerases appear capable of both types of reaction in vitro. Four DNA topoisomerases have been identified in Escherichia coli. Topoisomerase I, gyrase, and topoisomerase IV normally appear to have distinct essential functions within the cell. Gyrase and topoisomerase I are responsible for the regulation of DNA supercoiling. Both gyrase and topoisomerase IV are necessary for chromosomal decatenation. Multiple topoisomerases with distinct functions may give the cell more precise control over DNA topology by allowing tighter regulation of the principal enzymatic activities of these different proteins.
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Affiliation(s)
- A Luttinger
- Public Health Research Institute, New York, New York 10016, USA
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219
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Abstract
In the past year, the atomic structures of three fragments of type I DNA topoisomerases were elucidated. Together with the atomic structure of a fragment of bacterial gyrase, this wealth of structural information is helping to further our understanding of the mechanism of action of topoisomerases.
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Affiliation(s)
- A Sharma
- Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, IL 60208-3500, USA
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220
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221
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Nissen P, Reshetnikova L, Siboska G, Polekhina G, Thirup S, Kjeldgaard M, Clark BF, Nyborg J. Purification and crystallization of the ternary complex of elongation factor Tu:GTP and Phe-tRNA(Phe). FEBS Lett 1994; 356:165-8. [PMID: 7805830 DOI: 10.1016/0014-5793(94)01254-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Elongation factor Tu (EF-Tu) is the most abundant protein in prokaryotic cells. Its general function in protein biosynthesis is well established. It is a member of the large family of G-proteins, all of which bind guanosine phosphates (GDP or GTP) as cofactors. In its active GTP bound state EF-Tu binds aminoacylated tRNA (aa-tRNA) forming the ternary complex EF-Tu:GTP:aa-tRNA. The ternary complex interacts with the ribosome where the anticodon on tRNA recognises a codon on mRNA, GTPase activity is induced and inactive EF-Tu:GDP is released. Here we report the successful crystallization of a ternary complex of Thermus aquaticus EF-Tu:GDPNP and yeast Phe-tRNA(Phe) after its purification by HPLC.
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MESH Headings
- Chromatography, Gel
- Chromatography, High Pressure Liquid
- Crystallization
- Crystallography, X-Ray
- Electrophoresis, Polyacrylamide Gel
- Guanosine Triphosphate/chemistry
- Guanosine Triphosphate/isolation & purification
- Guanosine Triphosphate/metabolism
- Guanylyl Imidodiphosphate/metabolism
- Peptide Elongation Factor Tu/chemistry
- Peptide Elongation Factor Tu/isolation & purification
- Peptide Elongation Factor Tu/metabolism
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/isolation & purification
- RNA, Transfer, Phe/metabolism
- Saccharomyces cerevisiae/metabolism
- Thermus/metabolism
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Affiliation(s)
- P Nissen
- Department of Biostructural Chemistry, University of Aarhus, Denmark
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222
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Matsuo K, Silke J, Gramatikoff K, Schaffner W. The CpG-specific methylase SssI has topoisomerase activity in the presence of Mg2+. Nucleic Acids Res 1994; 22:5354-9. [PMID: 7816625 PMCID: PMC332082 DOI: 10.1093/nar/22.24.5354] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A prokaryotic CpG-specific methylase from Spiroplasma, SssI methylase, is now widely used to study the effect of CpG methylation in mammalian cells, and can processively modify cytosines in CpG dinucleotides in the absence of Mg2+. In the presence of Mg2+, we found (i) that the methylation reaction is distributive rather than processive as a result of the decreased affinity of SssI methylase for DNA, and (ii) that a type I-like topoisomerase activity is present in SssI methylase preparations. This topoisomerase activity was still present in SssI methylase further purified by either SDS-polyacrylamide or isoelectric focusing gel electrophoresis. We show that methylase and topoisomerase activities are not functionally interdependent, since conditions exist where only one or the other enzymatic activity is detectable. The catalytic domains of SssI methylase and prokaryotic topoisomerases show similarity at the amino acid level, further supporting the idea that the topoisomerase activity is a genuine activity of SssI methylase. Mycoplasmas, including Spiroplasma, have the smallest genomes of all living organisms; thus, this condensation of two enzymatic activities into the same protein may be a result of genome economy, and may also have functional implications for the mechanism of methylation.
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Affiliation(s)
- K Matsuo
- Institut für Molekularbiologie II, Universität Zürich, Switzerland
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223
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224
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Abstract
The ability of type II DNA topoisomerases to pass one DNA double helix through another can be explained by a mechanism involving two gates in the enzyme structure.
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Affiliation(s)
- G Orphanides
- Department of Biochemistry, University of Leicester, UK
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225
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Saintopin, a dual inhibitor of DNA topoisomerases I and II, as a probe for drug-enzyme interactions. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(19)61962-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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226
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Sharma A, Hanai R, Mondragón A. Crystal structure of the amino-terminal fragment of vaccinia virus DNA topoisomerase I at 1.6 A resolution. Structure 1994; 2:767-77. [PMID: 7994576 DOI: 10.1016/s0969-2126(94)00077-8] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
BACKGROUND Vaccinia virus, a cytoplasmically-replicating poxvirus, encodes a type I DNA topoisomerase that is biochemically similar to eukaryotic-like DNA topoisomerases I, and which has been widely studied as a model topoisomerase. It is the smallest topoisomerase known and is unusual in that it is resistant to the potent chemotherapeutic agent camptothecin. RESULTS The crystal structure of a 9 kDa amino-terminal fragment of vaccinia virus DNA topoisomerase I has been determined at 1.6 A resolution. The fragment forms a five-stranded, antiparallel beta-sheet with two short alpha-helices and connecting loops. Residues that are conserved between all eukaryotic-like type I topoisomerases are not clustered in particular regions of the structure. CONCLUSIONS This is the first atomic structure of any region of a eukaryotic-like DNA topoisomerase I. It has provided insights into the structural bases of the phenotypes of some single-site mutants of the intact topoisomerase. The structure has enabled us to study the interactions within a well-folded protein fragment and the camptothecin resistance of the viral topoisomerase.
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Affiliation(s)
- A Sharma
- Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, IL 60208-3500
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227
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Lee MH, Ohta T, Walker GC. A monocysteine approach for probing the structure and interactions of the UmuD protein. J Bacteriol 1994; 176:4825-37. [PMID: 8050995 PMCID: PMC196316 DOI: 10.1128/jb.176.16.4825-4837.1994] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
UmuD participates in a variety of protein-protein interactions that appear to be essential for its role in UV mutagenesis. To learn about these interactions, we have initiated an approach based on the construction of a series of monocysteine derivatives of UmuD and have carried out experiments exploring the chemistry of the unique thiol group in each derivative. In vivo and in vitro characterizations indicate that these proteins have an essentially native structure. In proposing a model for the interactions of UmuD in the homodimer, we have made the following assumptions: (i) the conformations of the mutant proteins are similar to that of the wild type, and (ii) the differences in reactivity of the mutant proteins are predominantly due to the positional effects of the single cysteine substitutions. The model proposes the following. The region including the Cys-24-Gly-25 cleavage site, Val-34, and Leu-44 are closer to the interface than the other positions tested as suggested by the relative ease of dimer cross-linking of the monocysteine derivatives at these positions by oxidation with iodine (I2) and by reaction with bis-maleimidohexane. The mutant with a Ser-to-Cys change at position 60 (SC60) is similar in iodoacetate reactivity to the preceding derivatives but cross-links less efficiently by I2 oxidation. This suggests that Ser-60, the site of the putative nucleophile in the cleavage reaction, is located further from the dimer interface or in a cleft region. Both Ser-19, located in the N-terminal fragment of UmuD that is removed by RecA-mediated cleavage, and Ser-67 are probably not as close to the dimer interface, since they are cross-linked more easily with bis-maleimidohexane than with I2. The SC67 mutant phenotype also suggests that this position is less important in RecA-mediated cleavage but more important in a subsequent role for UmuD in mutagenesis. Ala-89, Gln-100, and Asp-126 are probably not particularly solvent accessible and may play important roles in protein architecture.
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Affiliation(s)
- M H Lee
- Department of Biology, Massachusetts Institute of Technology, Cambridge 02139
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228
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Abstract
Proteins come in all sizes and shapes. Those which fold into a ring with a large hole in the middle may act as a clamp on DNA, a polysaccharide or another protein.
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Affiliation(s)
- J Janin
- Laboratoire de Biologie Structurale, UMR 9920 CNRS-Université Paris-Sud, Gif-sur-Yvette, France
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229
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Affiliation(s)
- C D Lima
- Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, Il 60208
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230
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231
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A happy diversity of interactions. NATURE STRUCTURAL BIOLOGY 1994; 1:129-30. [PMID: 7656025 DOI: 10.1038/nsb0394-129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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232
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Tse-Dinh YC. Biochemistry of bacterial type I DNA topoisomerases. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 1994; 29A:21-37. [PMID: 7826860 DOI: 10.1016/s1054-3589(08)60538-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Y C Tse-Dinh
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla 10595
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233
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Caron PR, Wang JC. Appendix. II: Alignment of primary sequences of DNA topoisomerases. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 1994; 29B:271-97. [PMID: 8996613 DOI: 10.1016/s1054-3589(08)61143-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- P R Caron
- Department of Biochemistry and Molecular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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