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Santoshi M, Engleng B, Eligar SM, Ratnakar IS, Nagamalleshwari E, Nagaraja V. Identification and characterization of a new HNH restriction endonuclease with unusual properties. Appl Microbiol Biotechnol 2023; 107:6263-6275. [PMID: 37626186 DOI: 10.1007/s00253-023-12717-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 07/20/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023]
Abstract
Restriction-modification (R-M) systems form a large superfamily constituting bacterial innate immunity mechanism. The restriction endonucleases (REases) are very diverse in subunit structure, DNA recognition, co-factor requirement, and mechanism of action. Among the different catalytic motifs, HNH active sites containing REases are the second largest group distinguished by the presence of the ββα-metal finger fold. KpnI is the first member of the HNH-family REases whose homologs are present in many bacteria of Enterobacteriaceae having varied degrees of sequence similarity between them. Considering that the homologs with a high similarity may have retained KpnI-like properties, while those with a low similarity could be different, we have characterized a distant KpnI homolog present in a pathogenic Klebsiella pneumoniae NTUH K2044. A comparison of the properties of KpnI and KpnK revealed that despite their similarity and the HNH motif, these two enzymes have different properties viz oligomerization, cleavage pattern, metal ion requirement, recognition sequence, and sequence specificity. Unlike KpnI, KpnK is a monomer in solution, nicks double-stranded DNA, recognizes degenerate sequence, and catalyses the degradation of DNA into smaller products after the initial cleavage at preferred sites. Due to several distinctive properties, it can be classified as a variant of the Type IIS enzyme having nicking endonuclease activity. KEY POINTS: • KpnK is a distant homolog of KpnI and belongs to the ββα-metal finger superfamily. • Both KpnI and KpnK have widespread occurrence in K. pneumoniae strains. • KpnK is a Type IIS restriction endonuclease with a single-strand nicking property.
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Affiliation(s)
- Meghna Santoshi
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Bharat Engleng
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Sachin M Eligar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Immadi Siva Ratnakar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Easa Nagamalleshwari
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India
| | - Valakunja Nagaraja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bengaluru, India.
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India.
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2
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Dudek CA, Jahn D. PRODORIC: state-of-the-art database of prokaryotic gene regulation. Nucleic Acids Res 2021; 50:D295-D302. [PMID: 34850133 PMCID: PMC8728284 DOI: 10.1093/nar/gkab1110] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/12/2021] [Accepted: 11/01/2021] [Indexed: 11/14/2022] Open
Abstract
PRODORIC is worldwide one of the largest collections of prokaryotic transcription factor binding sites from multiple bacterial sources with corresponding interpretation and visualization tools. With the introduction of PRODORIC2 in 2017, the transition to a modern web interface and maintainable backend was started. With this latest PRODORIC release the database backend is now fully API-based and provides programmatical access to the complete PRODORIC data. The visualization tools Genome Browser and ProdoNet from the original PRODORIC have been reintroduced and were integrated into the PRODORIC website. Missing input and output options from the original Virtual Footprint were added again for position weight matrix pattern-based searches. The whole PRODORIC dataset was reannotated. Every transcription factor binding site was re-evaluated to increase the overall database quality. During this process, additional parameters, like bound effectors, regulation type and different types of experimental evidence have been added for every transcription factor. Additionally, 109 new transcription factors and 6 new organisms have been added. PRODORIC is publicly available at https://www.prodoric.de.
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Affiliation(s)
- Christian-Alexander Dudek
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, Braunschweig D-38106, Germany
| | - Dieter Jahn
- Institute of Microbiology and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Rebenring 56, Braunschweig D-38106, Germany
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Slator C, Molphy Z, McKee V, Long C, Brown T, Kellett A. Di-copper metallodrugs promote NCI-60 chemotherapy via singlet oxygen and superoxide production with tandem TA/TA and AT/AT oligonucleotide discrimination. Nucleic Acids Res 2019; 46:2733-2750. [PMID: 29474633 PMCID: PMC5888725 DOI: 10.1093/nar/gky105] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/08/2018] [Indexed: 12/29/2022] Open
Abstract
In order to expand the current repertoire of cancer treatments and to help circumvent limitations associated with resistance, the identification of new metallodrugs with high potency and novel mechanisms of action is of significant importance. Here we present a class of di-copper(II) complex based on the synthetic chemical nuclease [Cu(Phen)2]+ (where Phen = 1,10-phenanthroline) that is selective against solid epithelial cancer cells from the National Cancer Institute's 60 human cell line panel (NCI-60). Two metallodrug leads are studied and in each case two [Cu(Phen)2]+ units are bridged by a dicarboxylate linker but the length and rigidity of the linkers differ distinctly. Both agents catalyze intracellular superoxide (O2•-) and singlet oxygen (1O2) formation with radical species mediating oxidative damage within nuclear DNA in the form of double strand breaks and to the mitochondria in terms of membrane depolarization. The complexes are effective DNA binders and can discriminate AT/AT from TA/TA steps of duplex DNA through induction of distinctive Z-like DNA or by intercalative interactions.
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Affiliation(s)
- Creina Slator
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Zara Molphy
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Vickie McKee
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Conor Long
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Tom Brown
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular Biotechnology, Dublin City University, Glasnevin, Dublin 9, Ireland
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Nbili W, Kaabi K, Lefebvre F, Fujita W, Jelsch C, Nasr CB. A Hirshfeld surface analysis, crystal structure, and physicochemical studies of a new Cu(II) complex with the 1,10-phenanthroline ligand. J COORD CHEM 2018. [DOI: 10.1080/00958972.2018.1489125] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Wijdene Nbili
- Faculté des Sciences de Bizerte, Laboratoire de Chimie des Matériaux, Université de Carthage, Zarzouna, Tunisie
| | - Kamel Kaabi
- Faculté des Sciences de Bizerte, Laboratoire de Chimie des Matériaux, Université de Carthage, Zarzouna, Tunisie
| | - Frédéric Lefebvre
- Laboratoire de Chimie Organométallique de Surface (LCOMS), Ecole Supérieure de Chimie Physique Electronique, Villeurbanne Cedex, France
| | - Wataru Fujita
- Graduate School of Natural Science, Nagoya City University, Yamanohata, Mizuho-cho, Mizuho-ku, Nagoya, Japan
| | - Christian Jelsch
- CRM2, CNRS, Institut Jean Barriol, Université de Lorraine, Vandoeuvre les Nancy, Cedex, France
| | - Cherif ben Nasr
- Faculté des Sciences de Bizerte, Laboratoire de Chimie des Matériaux, Université de Carthage, Zarzouna, Tunisie
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Sumrra SH, Mushtaq F, Khalid M, Raza MA, Nazar MF, Ali B, Braga AAC. Synthesis, spectral characterization and computed optical analysis of potent triazole based compounds. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 190:197-207. [PMID: 28922646 DOI: 10.1016/j.saa.2017.09.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 08/19/2017] [Accepted: 09/12/2017] [Indexed: 05/23/2023]
Abstract
Biologically active triazole Schiff base ligand (L) and metal complexes [Fe(II), Co(II), Ni(II), Cu(II) and Zn(II)] are reported herein. The ligand acted as tridentate and coordinated towards metallic ions via azomethine-N, triazolic-N moiety and deprotonated-O of phenyl substituents in an octahedral manner. These compounds were characterized by physical, spectral and analytical analysis. The synthesized ligand and metal complexes were screened for antibacterial pathogens against Chromohalobacter salexigens, Chromohalobacter israelensi, Halomonas halofila and Halomonas salina, antifungal bioassay against Aspergillus niger and Aspergellus flavin, antioxidant (DPPH, phosphomolybdate) and also for enzyme inhibition [butyrylcholinesterase (BChE) and acetylcholinesterase (AChE)] studies. The results of these activities indicated the ligand to possess potential activity which significantly increased upon chelation. Moreover, vibrational bands, frontier molecular orbitals (FMOs) and natural bond analysis (NBO) of ligand (1) were carried out through density functional theory (DFT) with B3lYP/6-311++G (d,p) approach. While, UV-Vis analysis was performed by time dependent TD-DFT with B3lYP/6-311++G (d,p) method. NBO analysis revealed that investigated compound (L) contains enormous molecular stability owing to hyper conjugative interactions. Theoretical spectroscopic findings showed good agreement to experimental spectroscopic data. Global reactivity descriptors were calculated using the energies of FMOs which indicated compound (L) might be bioactive. These parameters confirmed the charge transfer phenomenon and reasonable correspondence with experimental bioactivity results.
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Affiliation(s)
- Sajjad H Sumrra
- Department of Chemistry, University of Gujrat, Gujrat 50700, Pakistan.
| | - Fazila Mushtaq
- Department of Chemistry, University of Gujrat, Gujrat 50700, Pakistan
| | - Muhammad Khalid
- Department of Chemistry, University of Education Lahore, Faisalabad Campus, Pakistan; Department of Basic Sciences and Humanities, Khwaja Fareed University of Engineering & Information Technology, Rahim Yar Khan, Pakistan.
| | | | | | - Bakhat Ali
- Department of Basic Sciences and Humanities, Khwaja Fareed University of Engineering & Information Technology, Rahim Yar Khan, Pakistan
| | - Ataualpa A C Braga
- Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo 05508-000, Brazil
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6
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Chea EE, Jones LM. Analyzing the structure of macromolecules in their native cellular environment using hydroxyl radical footprinting. Analyst 2018; 143:798-807. [DOI: 10.1039/c7an01323j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Hydroxyl radical footprinting (HRF) has been successfully used to study the structure of both nucleic acids and proteins in live cells.
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Affiliation(s)
- Emily E. Chea
- Department of Pharmaceutical Sciences
- University of Maryland
- Baltimore
- USA
| | - Lisa M. Jones
- Department of Pharmaceutical Sciences
- University of Maryland
- Baltimore
- USA
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7
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Synthesis, spectral properties and DNA binding and nuclease activity of lanthanide (III) complexes of 2-benzoylpyridine benzhydrazone: X-ray crystal structure, Hirshfeld studies and nitrate-π interactions of cerium(III) complex. J CHEM SCI 2016. [DOI: 10.1007/s12039-015-1003-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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8
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Kotha S, E. Shirbhate M, Kumar Chinnam A, Sreevani G. Synthesis of Phenanthroline and Indole Based Hybrid Cyclophane Derivatives via Ring-Closing Metathesis. HETEROCYCLES 2016. [DOI: 10.3987/com-15-s(t)18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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9
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Raja K, Suseelamma A, Reddy KH. Synthesis, spectral properties, DNA binding interactions and DNA cleavage studies of lanthanide (III) complexes of 2-acetylpyridine acetoylhydrazone: the X-ray crystal structure of 10-coordinate Ce (III) and Sm (III) complexes. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2015. [DOI: 10.1007/s13738-015-0624-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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10
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Larragy R, Fitzgerald J, Prisecaru A, McKee V, Leonard P, Kellett A. Protein engineering with artificial chemical nucleases. Chem Commun (Camb) 2015; 51:12908-11. [DOI: 10.1039/c5cc04615g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The process of protein engineering using artificial chemical nucleases is reported using the Cu(ii)-bis-1,10-phenanthroline complex.
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Affiliation(s)
- Ruth Larragy
- Biomedical Diagnostics Institute
- Dublin City University
- Dublin 9
- Ireland
| | - Jenny Fitzgerald
- Biomedical Diagnostics Institute
- Dublin City University
- Dublin 9
- Ireland
| | - Andreea Prisecaru
- School of Chemical Sciences and National Institute for Cellular Biotechnology
- Dublin City University
- Dublin 9
- Ireland
| | - Vickie McKee
- School of Chemical Sciences and National Institute for Cellular Biotechnology
- Dublin City University
- Dublin 9
- Ireland
| | - Paul Leonard
- Biomedical Diagnostics Institute
- Dublin City University
- Dublin 9
- Ireland
| | - Andrew Kellett
- School of Chemical Sciences and National Institute for Cellular Biotechnology
- Dublin City University
- Dublin 9
- Ireland
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11
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Porter MR, Kochi A, Karty JA, Lim MH, Zaleski JM. Chelation-induced diradical formation as an approach to modulation of the amyloid-β aggregation pathway. Chem Sci 2014; 6:1018-1026. [PMID: 29560189 PMCID: PMC5811126 DOI: 10.1039/c4sc01979b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 10/30/2014] [Indexed: 11/21/2022] Open
Abstract
Current approaches toward modulation of metal-induced Aβ aggregation pathways involve the development of small molecules that bind metal ions, such as Cu(ii) and Zn(ii), and interact with Aβ. For this effort, we present the enediyne-containing ligand (Z)-N,N'-bis[1-pyridin-2-yl-meth(E)-ylidene]oct-4-ene-2,6-diyne-1,8-diamine (PyED), which upon chelation of Cu(ii) and Zn(ii) undergoes Bergman-cyclization to yield diradical formation. The ability of this chelation-triggered diradical to modulate Aβ aggregation is evaluated relative to the non-radical generating control pyridine-2-ylmethyl-(2-{[(pyridine-2-ylmethylene)-amino]-methyl}-benzyl)-amine (PyBD). Variable-pH, ligand UV-vis titrations reveal pKa = 3.81(2) for PyBD, indicating it exists mainly in the neutral form at experimental pH. Lipinski's rule parameters and evaluation of blood-brain barrier (BBB) penetration potential by the PAMPA-BBB assay suggest that PyED may be CNS+ and penetrate the BBB. Both PyED and PyBD bind Zn(ii) and Cu(ii) as illustrated by bathochromic shifts of their UV-vis features. Speciation diagrams indicate that Cu(ii)-PyBD is the major species at pH 6.6 with a nanomolar Kd, suggesting the ligand may be capable of interacting with Cu(ii)-Aβ species. In the presence of Aβ40/42 under hyperthermic conditions (43 °C), the radical-generating PyED demonstrates markedly enhanced activity (2-24 h) toward the modulation of Aβ species as determined by gel electrophoresis. Correspondingly, transmission electron microscopy images of these samples show distinct morphological changes to the fibril structure that are most prominent for Cu(ii)-Aβ cases. The loss of CO2 from the metal binding region of Aβ in MALDI-TOF mass spectra further suggests that metal-ligand-Aβ interaction with subsequent radical formation may play a role in the aggregation pathway modulation.
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Affiliation(s)
- Meghan R Porter
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , USA .
| | - Akiko Kochi
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , USA.,Department of Chemistry , Ulsan National Institute of Science and Technology (UNIST) , Ulsan 689-798 , Korea .
| | - Jonathan A Karty
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , USA .
| | - Mi Hee Lim
- Department of Chemistry , Ulsan National Institute of Science and Technology (UNIST) , Ulsan 689-798 , Korea . .,Life Sciences Institute , University of Michigan , Ann Arbor , Michigan 48109 , USA
| | - Jeffrey M Zaleski
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , USA .
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He G, Vasilieva E, Bashkin JK, Dupureur CM. Mapping small DNA ligand hydroxyl radical footprinting and affinity cleavage products for capillary electrophoresis. Anal Biochem 2013; 439:99-101. [PMID: 23608054 PMCID: PMC3713177 DOI: 10.1016/j.ab.2013.04.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/08/2013] [Accepted: 04/10/2013] [Indexed: 12/17/2022]
Abstract
The mapping of DNA footprints and affinity cleavage sites for small DNA ligands is affected by the choice of sequencing chemistry and end label, and the potential for indexing errors can be significant when mapping small ligand-DNA interactions. Described here is a mechanism for avoiding such errors based on a summary of standard labeling, cleavage, and indexing chemistries and a comparison among them for analysis of these interactions by capillary electrophoresis. The length dependence of the difference between Sanger and Maxam-Gilbert indexing is examined for a number of duplexes of mixed sequence.
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Affiliation(s)
- Gaofei He
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121
| | - Elena Vasilieva
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121
| | - James K. Bashkin
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121
| | - Cynthia M. Dupureur
- Department of Chemistry & Biochemistry and the Center for Nanoscience, University of Missouri St. Louis, St. Louis, MO 63121
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13
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Xu G, Chance MR. Hydroxyl Radical-Mediated Modification of Proteins as Probes for Structural Proteomics. Chem Rev 2007; 107:3514-43. [PMID: 17683160 DOI: 10.1021/cr0682047] [Citation(s) in RCA: 513] [Impact Index Per Article: 30.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guozhong Xu
- Center for Proteomics, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
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Adilakshmi T, Lease RA, Woodson SA. Hydroxyl radical footprinting in vivo: mapping macromolecular structures with synchrotron radiation. Nucleic Acids Res 2006; 34:e64. [PMID: 16682443 PMCID: PMC1458516 DOI: 10.1093/nar/gkl291] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
We used a high flux synchrotron X-ray beam to map the structure of 16S rRNA and RNase P in viable bacteria in situ. A 300 ms exposure to the X-ray beam was sufficient for optimal cleavage of the phosphodiester backbone. The in vivo footprints of the 16S rRNA in frozen cells were similar to those obtained in vitro and were consistent with the predicted accessibility of the RNA backbone to hydroxyl radical. Protection or enhanced cleavage of certain nucleotides in vivo can be explained by interactions with tRNA and perturbation of the subunit interface. Thus, short exposures to a synchrotron X-ray beam can footprint the tertiary structure and protein contacts of RNA–protein complexes with nucleotide resolution in living cells.
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Affiliation(s)
| | | | - Sarah A. Woodson
- To whom correspondence should be addressed. Tel: +1 410 516 2015; Fax: +1 410 516 4118;
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Zinoviev VV, Yakishchik SI, Evdokimov AA, Malygin EG, Hattman S. Symmetry elements in DNA structure important for recognition/methylation by DNA [amino]-methyltransferases. Nucleic Acids Res 2004; 32:3930-4. [PMID: 15280508 PMCID: PMC506800 DOI: 10.1093/nar/gkh712] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The phage T4Dam and EcoDam DNA-[adenine-N6] methyltransferases (MTases) methylate GATC palindromic sequences, while the BamHI DNA-[cytosine-N4] MTase methylates the GGATCC palindrome (which contains GATC) at the internal cytosine residue. We compared the ability of these enzymes to interact productively with defective duplexes in which individual elements were deleted on one chain. A sharp decrease in kcat was observed for all three enzymes if a particular element of structural symmetry was disrupted. For the BamHI MTase, integrity of the ATCC was critical, while an intact GAT sequence was necessary for the activity of T4Dam, and an intact GA was necessary for EcoDam. Theoretical alignment of the region of best contacts between the protein and DNA showed that in the case of a palindromic interaction site, a zone covering the 5'-symmetric residues is located in the major groove versus a zone of contact covering the 3'-symmetric residues in the minor groove. Our data fit a simple rule of thumb that the most important contacts are aligned around the methylation target base: if the target base is in the 5' half of the palindrome, the interaction between the enzyme and the DNA occurs mainly in the major groove; if it is in the 3' half, the interaction occurs mainly in the minor groove.
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Affiliation(s)
- Victor V Zinoviev
- Institute of Molecular Biology, State Research Center of Virology and Biotechnology Vector, Novosibirsk 630559, Russia
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Chandrashekaran S, Manjunatha UH, Nagaraja V. KpnI restriction endonuclease and methyltransferase exhibit contrasting mode of sequence recognition. Nucleic Acids Res 2004; 32:3148-55. [PMID: 15192117 PMCID: PMC434444 DOI: 10.1093/nar/gkh638] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The molecular basis of the interaction of KpnI restriction endonuclease (REase) and the corresponding methyltransferase (MTase) at their cognate recognition sequence is investigated using a range of footprinting techniques. DNase I protection analysis with the REase reveals the protection of a 14-18 bp region encompassing the hexanucleotide recognition sequence. The MTase, in contrast, protects a larger region. KpnI REase contacts two adjacent guanine residues and the single adenine residue in both the strands within the recognition sequence 5'-GGTACC-3', inferred by dimethylsulfate (DMS) protection, interference and missing nucleotide interference analysis. In contrast, KpnI MTase does not show elaborate base-specific contacts. Ethylation interference analysis also showed the differential interaction of REase and MTase with phosphate groups of three adjacent bases on both strands within the recognition sequence. The single thymine residue within the sequence is hyper- reactive to the permanganate oxidation, consistent with MTase-induced base flipping. The REase on the other hand does not show any major DNA distortion. The results demonstrate that the differences in the molecular interaction pattern of the two proteins at the same recognition sequence reflect the contrasting chemistry of DNA cleavage and methylation catalyzed by these two dissimilar enzymes, working in combination as constituents of a cellular defense strategy.
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DNA and RNA Cleavage Mediated by Phenanthroline-Cuprous Oligonucleotides: From Properties to Applications. ARTIFICIAL NUCLEASES 2004. [DOI: 10.1007/978-3-642-18510-6_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
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18
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Copper Containing Nuclease Mimics: Synthetic Models and Biochemical Applications. ARTIFICIAL NUCLEASES 2004. [DOI: 10.1007/978-3-642-18510-6_9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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