Function inferences from a molecular structural model of bacterial ParE toxin
Main Author: | |
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Publication Date: | 2010 |
Other Authors: | , , , |
Format: | Article |
Language: | eng |
Source: | Repositório Institucional da UNESP |
Download full: | http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2951705/ http://hdl.handle.net/11449/123448 |
Summary: | Toxin-antitoxin (TA) systems contribute to plasmid stability by a mechanism that relies on the differential stabilities of the toxin and antitoxin proteins and leads to the killing of daughter bacteria that did not receive a plasmid copy at the cell division. ParE is the toxic component of a TA system that constitutes along with RelE an important class of bacterial toxin called RelE/ParE superfamily. For ParE toxin, no crystallographic structure is available so far and rare in vitro studies demonstrated that the target of toxin activity is E. coli DNA gyrase. Here, a 3D Model for E. coli ParE toxin by molecular homology modeling was built using MODELLER, a program for comparative modeling. The Model was energy minimized by CHARMM and validated using PROCHECK and VERIFY3D programs. Resulting Ramachandran plot analysis it was found that the portion residues failing into the most favored and allowed regions was 96.8%. Structural similarity search employing DALI server showed as the best matches RelE and YoeB families. The Model also showed similarities with other microbial ribonucleases but in a small score. A possible homologous deep cleft active site was identified in the Model using CASTp program. Additional studies to investigate the nuclease activity in members of ParE family as well as to confirm the inhibitory replication activity are needed. The predicted Model allows initial inferences about the unexplored 3D structure of the ParE toxin and may be further used in rational design of molecules for structurefunction studies. |
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Function inferences from a molecular structural model of bacterial ParE toxinParE toxinTA systemsRelE/ParE superfamilyHomology modelingToxin-antitoxin (TA) systems contribute to plasmid stability by a mechanism that relies on the differential stabilities of the toxin and antitoxin proteins and leads to the killing of daughter bacteria that did not receive a plasmid copy at the cell division. ParE is the toxic component of a TA system that constitutes along with RelE an important class of bacterial toxin called RelE/ParE superfamily. For ParE toxin, no crystallographic structure is available so far and rare in vitro studies demonstrated that the target of toxin activity is E. coli DNA gyrase. Here, a 3D Model for E. coli ParE toxin by molecular homology modeling was built using MODELLER, a program for comparative modeling. The Model was energy minimized by CHARMM and validated using PROCHECK and VERIFY3D programs. Resulting Ramachandran plot analysis it was found that the portion residues failing into the most favored and allowed regions was 96.8%. Structural similarity search employing DALI server showed as the best matches RelE and YoeB families. The Model also showed similarities with other microbial ribonucleases but in a small score. A possible homologous deep cleft active site was identified in the Model using CASTp program. Additional studies to investigate the nuclease activity in members of ParE family as well as to confirm the inhibitory replication activity are needed. The predicted Model allows initial inferences about the unexplored 3D structure of the ParE toxin and may be further used in rational design of molecules for structurefunction studies.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Universidade Estadual Paulista Júlio de Mesquita Filho, Departamento de Bioquímica e Tecnologia Química, Instituto de Química de Araraquara, Araraquara, Rua Professor Francisco Degni, nº 55, Quitandinha, CEP 14800-900, SP, BrasilUniversidade Estadual Paulista Júlio de Mesquita Filho, Departamento de Bioquímica e Tecnologia Química, Instituto de Química de Araraquara, Araraquara, Rua Professor Francisco Degni, nº 55, Quitandinha, CEP 14800-900, SP, BrasilUniversidade Estadual Paulista (Unesp)Barbosa, Luiz Carlos Bertucci [UNESP]Garrido, Saulo Santesso [UNESP]Garcia, Anderson [UNESP]Delfino, Davi Barbosa [UNESP]Marchetto, Reinaldo [UNESP]2015-05-15T13:30:13Z2015-05-15T13:30:13Z2010info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article438-440application/pdfhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC2951705/Bioinformation, v. 4, n. 10, p. 438-440, 2010.0973-2063http://hdl.handle.net/11449/123448ISSN0973-2063-2010-4-10-438-440.pdf3572731191643273571118225164110341530938805818740613179867992921Currículo Lattesreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengBioinformationinfo:eu-repo/semantics/openAccess2023-12-25T06:18:54Zoai:repositorio.unesp.br:11449/123448Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462024-08-05T21:14:11.304101Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Function inferences from a molecular structural model of bacterial ParE toxin |
title |
Function inferences from a molecular structural model of bacterial ParE toxin |
spellingShingle |
Function inferences from a molecular structural model of bacterial ParE toxin Barbosa, Luiz Carlos Bertucci [UNESP] ParE toxin TA systems RelE/ParE superfamily Homology modeling |
title_short |
Function inferences from a molecular structural model of bacterial ParE toxin |
title_full |
Function inferences from a molecular structural model of bacterial ParE toxin |
title_fullStr |
Function inferences from a molecular structural model of bacterial ParE toxin |
title_full_unstemmed |
Function inferences from a molecular structural model of bacterial ParE toxin |
title_sort |
Function inferences from a molecular structural model of bacterial ParE toxin |
author |
Barbosa, Luiz Carlos Bertucci [UNESP] |
author_facet |
Barbosa, Luiz Carlos Bertucci [UNESP] Garrido, Saulo Santesso [UNESP] Garcia, Anderson [UNESP] Delfino, Davi Barbosa [UNESP] Marchetto, Reinaldo [UNESP] |
author_role |
author |
author2 |
Garrido, Saulo Santesso [UNESP] Garcia, Anderson [UNESP] Delfino, Davi Barbosa [UNESP] Marchetto, Reinaldo [UNESP] |
author2_role |
author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) |
dc.contributor.author.fl_str_mv |
Barbosa, Luiz Carlos Bertucci [UNESP] Garrido, Saulo Santesso [UNESP] Garcia, Anderson [UNESP] Delfino, Davi Barbosa [UNESP] Marchetto, Reinaldo [UNESP] |
dc.subject.por.fl_str_mv |
ParE toxin TA systems RelE/ParE superfamily Homology modeling |
topic |
ParE toxin TA systems RelE/ParE superfamily Homology modeling |
description |
Toxin-antitoxin (TA) systems contribute to plasmid stability by a mechanism that relies on the differential stabilities of the toxin and antitoxin proteins and leads to the killing of daughter bacteria that did not receive a plasmid copy at the cell division. ParE is the toxic component of a TA system that constitutes along with RelE an important class of bacterial toxin called RelE/ParE superfamily. For ParE toxin, no crystallographic structure is available so far and rare in vitro studies demonstrated that the target of toxin activity is E. coli DNA gyrase. Here, a 3D Model for E. coli ParE toxin by molecular homology modeling was built using MODELLER, a program for comparative modeling. The Model was energy minimized by CHARMM and validated using PROCHECK and VERIFY3D programs. Resulting Ramachandran plot analysis it was found that the portion residues failing into the most favored and allowed regions was 96.8%. Structural similarity search employing DALI server showed as the best matches RelE and YoeB families. The Model also showed similarities with other microbial ribonucleases but in a small score. A possible homologous deep cleft active site was identified in the Model using CASTp program. Additional studies to investigate the nuclease activity in members of ParE family as well as to confirm the inhibitory replication activity are needed. The predicted Model allows initial inferences about the unexplored 3D structure of the ParE toxin and may be further used in rational design of molecules for structurefunction studies. |
publishDate |
2010 |
dc.date.none.fl_str_mv |
2010 2015-05-15T13:30:13Z 2015-05-15T13:30:13Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2951705/ Bioinformation, v. 4, n. 10, p. 438-440, 2010. 0973-2063 http://hdl.handle.net/11449/123448 ISSN0973-2063-2010-4-10-438-440.pdf 3572731191643273 5711182251641103 4153093880581874 0613179867992921 |
url |
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2951705/ http://hdl.handle.net/11449/123448 |
identifier_str_mv |
Bioinformation, v. 4, n. 10, p. 438-440, 2010. 0973-2063 ISSN0973-2063-2010-4-10-438-440.pdf 3572731191643273 5711182251641103 4153093880581874 0613179867992921 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Bioinformation |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
438-440 application/pdf |
dc.source.none.fl_str_mv |
Currículo Lattes reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
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1808129300117848064 |