ArticleNucleic acids research2007
Topology of Type II REases revisited; structural classes and the common conserved core.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 36 citations in OpenAlex.
- Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI.Nucleic acids research · 2019Article
- Rpn (YhgA-Like) Proteins of Escherichia coli K-12 and Their Contribution to RecA-Independent Horizontal Transfer.Journal of bacteriology · 2017Article
- Interdomain communication in the endonuclease/motor subunit of type I restriction-modification enzyme EcoR124I.Journal of molecular modeling · 2014Article
- Type II restriction endonucleases--a historical perspective and more.Nucleic acids research · 2014Review
- Structure and mutagenesis of the DNA modification-dependent restriction endonuclease AspBHI.Scientific reports · 2014Article
- Probabilistic approach to predicting substrate specificity of methyltransferases.PLoS computational biology · 2014Article
- Type I restriction enzymes and their relatives.Nucleic acids research · 2014Review
- Recognition of an expanded genetic alphabet by type-II restriction endonucleases and their application to analyze polymerase fidelity.Nucleic acids research · 2011Article
- Nucleases: diversity of structure, function and mechanism.Quarterly reviews of biophysics · 2011Review
- DNA intercalation without flipping in the specific ThaI-DNA complex.Nucleic acids research · 2011Article
- The crystal structure of D212 from sulfolobus spindle-shaped virus ragged hills reveals a new member of the PD-(D/E)XK nuclease superfamily.Journal of virology · 2010Article
- Structural mechanisms for the 5'-CCWGG sequence recognition by the N- and C-terminal domains of EcoRII.Nucleic acids research · 2009Article
- The MmeI family: type II restriction-modification enzymes that employ single-strand modification for host protection.Nucleic acids research · 2009Article
- Activity and specificity of the bacterial PD-(D/E)XK homing endonuclease I-Ssp6803I.Journal of molecular biology · 2009Article
- Cleavage of mispaired heteroduplex DNA substrates by numerous restriction enzymes.Current issues in molecular biology · 2009Article
- Structure of the motor subunit of type I restriction-modification complex EcoR124I.Nature structural & molecular biology · 2009Article
- Functional analysis of MmeI from methanol utilizer Methylophilus methylotrophus, a subtype IIC restriction-modification enzyme related to type I enzymes.Applied and environmental microbiology · 2009Article
- Early interrogation and recognition of DNA sequence by indirect readout.Structure (London, England : 1993) · 2008Article
- Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses.Nucleic acids research · 2008Article
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
Type II restriction endonucleases (REases) are deoxyribonucleases that cleave DNA sequences with remarkable specificity. Type II REases are highly divergent in sequence as well as in topology, i.e. the connectivity of secondary structure elements. A widely held assumption is that a structural core of five beta-strands flanked by two alpha-helices is common to these enzymes. We introduce a systematic procedure to enumerate secondary structure elements in an unambiguous and reproducible way, and use it to analyze the currently available X-ray structures of Type II REases. Based on this analysis, we propose an alternative definition of the core, which we term the alphabetaalpha-core. The alphabetaalpha-core includes the most frequently observed secondary structure elements and is not a sandwich, as it consists of a five-strand beta-sheet and two alpha-helices on the same face of the beta-sheet. We use the alphabetaalpha-core connectivity as a basis for grouping the Type II REases into distinct structural classes. In these new structural classes, the connectivity correlates with the angles between the secondary structure elements and with the cleavage patterns of the REases. We show that there exists a substructure of the alphabetaalpha-core, namely a common conserved core, ccc, defined here as one alpha-helix and four beta-strands common to all Type II REase of known structure.
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