Topology of Type II REases revisited; structural classes and the common conserved core

Autores
Niv, Masha Y.; Ripoll, Daniel R.; Vila, Jorge Alberto; Liwo, Adam; Vanamee, Éva S.; Aggarwal, Aneel K.; Weinstein, Harel; Scheraga, Harold A.
Año de publicación
2007
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
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 β-strands flanked by two α-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 αβα-core. The αβα-core includes the most frequently observed secondary structure elements and is not a sandwich, as it consists of a five-strand β-sheet and two α-helices on the same face of the β-sheet. We use the αβα-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 αβα-core, namely a common conserved core, ccc, defined here as one α-helix and four β-strands common to all Type II REase of known structure.
Fil: Niv, Masha Y.. Cornell University; Estados Unidos
Fil: Ripoll, Daniel R.. Cornell Theory Center; Estados Unidos
Fil: Vila, Jorge Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; Argentina
Fil: Liwo, Adam. Cornell University; Estados Unidos
Fil: Vanamee, Éva S.. Mount Sinai School of Medicine; Estados Unidos
Fil: Aggarwal, Aneel K.. Mount Sinai School of Medicine; Estados Unidos
Fil: Weinstein, Harel. Cornell University; Estados Unidos
Fil: Scheraga, Harold A.. Cornell University; Estados Unidos
Materia
REASES
CLEAVE DNA
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/119675
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/119675
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repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Topology of Type II REases revisited; structural classes and the common conserved coreNiv, Masha Y.Ripoll, Daniel R.Vila, Jorge AlbertoLiwo, AdamVanamee, Éva S.Aggarwal, Aneel K.Weinstein, HarelScheraga, Harold A.REASESCLEAVE DNAhttps://purl.org/becyt/ford/1.3https://purl.org/becyt/ford/1Type 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 β-strands flanked by two α-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 αβα-core. The αβα-core includes the most frequently observed secondary structure elements and is not a sandwich, as it consists of a five-strand β-sheet and two α-helices on the same face of the β-sheet. We use the αβα-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 αβα-core, namely a common conserved core, ccc, defined here as one α-helix and four β-strands common to all Type II REase of known structure.Fil: Niv, Masha Y.. Cornell University; Estados UnidosFil: Ripoll, Daniel R.. Cornell Theory Center; Estados UnidosFil: Vila, Jorge Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; ArgentinaFil: Liwo, Adam. Cornell University; Estados UnidosFil: Vanamee, Éva S.. Mount Sinai School of Medicine; Estados UnidosFil: Aggarwal, Aneel K.. Mount Sinai School of Medicine; Estados UnidosFil: Weinstein, Harel. Cornell University; Estados UnidosFil: Scheraga, Harold A.. Cornell University; Estados UnidosOxford University Press2007-04info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/119675Niv, Masha Y.; Ripoll, Daniel R.; Vila, Jorge Alberto; Liwo, Adam; Vanamee, Éva S.; et al.; Topology of Type II REases revisited; structural classes and the common conserved core; Oxford University Press; Nucleic Acids Research; 35; 7; 4-2007; 2227-22370305-10481362-4962CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gkm045info:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/nar/article/35/7/2227/1086673info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:54:06Zoai:ri.conicet.gov.ar:11336/119675instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-09-29 09:54:06.289CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Topology of Type II REases revisited; structural classes and the common conserved core
title Topology of Type II REases revisited; structural classes and the common conserved core
spellingShingle Topology of Type II REases revisited; structural classes and the common conserved core
Niv, Masha Y.
REASES
CLEAVE DNA
title_short Topology of Type II REases revisited; structural classes and the common conserved core
title_full Topology of Type II REases revisited; structural classes and the common conserved core
title_fullStr Topology of Type II REases revisited; structural classes and the common conserved core
title_full_unstemmed Topology of Type II REases revisited; structural classes and the common conserved core
title_sort Topology of Type II REases revisited; structural classes and the common conserved core
dc.creator.none.fl_str_mv Niv, Masha Y.
Ripoll, Daniel R.
Vila, Jorge Alberto
Liwo, Adam
Vanamee, Éva S.
Aggarwal, Aneel K.
Weinstein, Harel
Scheraga, Harold A.
author Niv, Masha Y.
author_facet Niv, Masha Y.
Ripoll, Daniel R.
Vila, Jorge Alberto
Liwo, Adam
Vanamee, Éva S.
Aggarwal, Aneel K.
Weinstein, Harel
Scheraga, Harold A.
author_role author
author2 Ripoll, Daniel R.
Vila, Jorge Alberto
Liwo, Adam
Vanamee, Éva S.
Aggarwal, Aneel K.
Weinstein, Harel
Scheraga, Harold A.
author2_role author
author
author
author
author
author
author
dc.subject.none.fl_str_mv REASES
CLEAVE DNA
topic REASES
CLEAVE DNA
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.3
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv 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 β-strands flanked by two α-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 αβα-core. The αβα-core includes the most frequently observed secondary structure elements and is not a sandwich, as it consists of a five-strand β-sheet and two α-helices on the same face of the β-sheet. We use the αβα-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 αβα-core, namely a common conserved core, ccc, defined here as one α-helix and four β-strands common to all Type II REase of known structure.
Fil: Niv, Masha Y.. Cornell University; Estados Unidos
Fil: Ripoll, Daniel R.. Cornell Theory Center; Estados Unidos
Fil: Vila, Jorge Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; Argentina
Fil: Liwo, Adam. Cornell University; Estados Unidos
Fil: Vanamee, Éva S.. Mount Sinai School of Medicine; Estados Unidos
Fil: Aggarwal, Aneel K.. Mount Sinai School of Medicine; Estados Unidos
Fil: Weinstein, Harel. Cornell University; Estados Unidos
Fil: Scheraga, Harold A.. Cornell University; Estados Unidos
description 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 β-strands flanked by two α-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 αβα-core. The αβα-core includes the most frequently observed secondary structure elements and is not a sandwich, as it consists of a five-strand β-sheet and two α-helices on the same face of the β-sheet. We use the αβα-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 αβα-core, namely a common conserved core, ccc, defined here as one α-helix and four β-strands common to all Type II REase of known structure.
publishDate 2007
dc.date.none.fl_str_mv 2007-04
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/119675
Niv, Masha Y.; Ripoll, Daniel R.; Vila, Jorge Alberto; Liwo, Adam; Vanamee, Éva S.; et al.; Topology of Type II REases revisited; structural classes and the common conserved core; Oxford University Press; Nucleic Acids Research; 35; 7; 4-2007; 2227-2237
0305-1048
1362-4962
CONICET Digital
CONICET
url http://hdl.handle.net/11336/119675
identifier_str_mv Niv, Masha Y.; Ripoll, Daniel R.; Vila, Jorge Alberto; Liwo, Adam; Vanamee, Éva S.; et al.; Topology of Type II REases revisited; structural classes and the common conserved core; Oxford University Press; Nucleic Acids Research; 35; 7; 4-2007; 2227-2237
0305-1048
1362-4962
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/doi/10.1093/nar/gkm045
info:eu-repo/semantics/altIdentifier/url/https://academic.oup.com/nar/article/35/7/2227/1086673
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Oxford University Press
publisher.none.fl_str_mv Oxford University Press
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 13.070432

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