Substrate-binding cavities in OBPs of the Ami system and comparison with related proteins [Dataset]
(A) The bound peptides visualized inside the binding cavity of OBPs belonging to the Ami permease reveal the extent of the unoccupied space. The cavity is shown as a gray semi-transparent surface, the peptide is shown in yellow capped stick, and the protein is not shown. AmiA:5, AmiA in complex with...
| Autores: | , , , , , , , , , , , , , , , , , |
|---|---|
| Tipo de recurso: | conjunto de datos |
| Estado: | Versión publicada |
| Fecha de publicación: | 2024 |
| País: | España |
| Institución: | Consejo Superior de Investigaciones Científicas (CSIC) |
| Repositorio: | DIGITAL.CSIC. Repositorio Institucional del CSIC |
| OAI Identifier: | oai:digital.csic.es:10261/374492 |
| Acceso en línea: | http://hdl.handle.net/10261/374492 |
| Access Level: | acceso abierto |
| Palabra clave: | Unexpected remarkable promiscuity Streptococcus pneumoniae </ Produced de novo Multiple crystallographic structures Escherichia coli </ Diverse peptide specificities Closed conformations along Certain amino acids >, displaying affinity Ensure sufficient uptake Mass spectrometry analysis div >< p Orchestrating oligopeptide uptake Four proteins building Ami transporter system Abc transporter channel Pneumococci Structural analysis Oligopeptide recognition Oligopeptide binding Uptake mechanism Wide range Vivo implications Transport systems Substantial array Structural basis Silico modelling Shedding light Oligopeptides demonstrates Invasive infections Energy balance Cellular cytoplasm Cell surface Binding cassette Becomes indispensable Auxotrophic nature Abc transporters |
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oai:digital.csic.es:10261/374492 |
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Substrate-binding cavities in OBPs of the Ami system and comparison with related proteins [Dataset]Alcorlo, MartínAbdullah, Mohammed R.Steil, LeifSotomayor, FranciscoLópez de Oro, LauraCastro, Sonia deVelázquez, SonsolesKohler, Thomas P.Jiménez, ElisabetMedina, AnaUsón, IsabelKeller, Lance E.Bradshaw, Jessica L.McDaniel, Larry S.Camarasa Rius, María JoséVölker, UweHammerschmidt, SvenHermoso, Juan A.Unexpected remarkable promiscuityStreptococcus pneumoniae </Produced de novoMultiple crystallographic structuresEscherichia coli </Diverse peptide specificitiesClosed conformations alongCertain amino acids>, displaying affinityEnsure sufficient uptakeMass spectrometry analysisdiv >< pOrchestrating oligopeptide uptakeFour proteins buildingAmi transporter systemAbc transporter channelPneumococciStructural analysisOligopeptide recognitionOligopeptide bindingUptake mechanismWide rangeVivo implicationsTransport systemsSubstantial arrayStructural basisSilico modellingShedding lightOligopeptides demonstratesInvasive infectionsEnergy balanceCellular cytoplasmCell surfaceBinding cassetteBecomes indispensableAuxotrophic natureAbc transporters(A) The bound peptides visualized inside the binding cavity of OBPs belonging to the Ami permease reveal the extent of the unoccupied space. The cavity is shown as a gray semi-transparent surface, the peptide is shown in yellow capped stick, and the protein is not shown. AmiA:5, AmiA in complex with peptide 5; AliD:1, AliD in complex with peptide 1; AliB:2, AliB in complex with peptide 2; AmiB:3, AmiB in complex with peptide 3 and AmiB:4, AmiB in complex with peptide 4. (B) Comparison of the binding cavity volumes found on SBPs of the Ami permease, including the cavities of OppA from L. lactis [PDB 3DRF [30]], AppA from B. subtillis (PDB 1XOC [31]), OppA from S. typhimurium [PDB 1B4Z [26]], DppA [PDB 1DPE] and ProX from E. coli [PDB 1SW2 [33]], for comparative purposes. The volumes were calculated with the program POCASA v1.1 [34] using default parameters and a Probe Radius of 1 Å.Peer reviewedPublic Library of ScienceConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202420242024info:eu-repo/semantics/datasethttp://purl.org/coar/resource_type/c_ddb1Publisher's versioninfo:eu-repo/semantics/publishedVersionimage/tiffhttp://hdl.handle.net/10261/374492reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)InglésAlcorlo, Martín; Abdullah, Mohammed R.; Steil, Leif; Sotomayor, Francisco; López de Oro, Laura; Castro, Sonia de ; Velázquez, Sonsoles; Kohler, Thomas P.; Jiménez, Elisabet; Medina, Ana; Usón, Isabel; Keller, Lance E.; Bradshaw, Jessica L..; McDaniel, Larry S.; Camarasa Rius, María José; Völker, Uwe; Hammerschmidt, Sven; Hermoso, Juan A. Molecular and structural basis of oligopeptide recognition by the Ami transporter system in pneumococci. https://doi.org/10.1371/journal.ppat.1011883 . http://hdl.handle.net/10261/364789https://doi.org/10.1371/journal.ppat.1011883.s024Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3744922026-05-22T06:33:51Z |
| dc.title.none.fl_str_mv |
Substrate-binding cavities in OBPs of the Ami system and comparison with related proteins [Dataset] |
| title |
Substrate-binding cavities in OBPs of the Ami system and comparison with related proteins [Dataset] |
| spellingShingle |
Substrate-binding cavities in OBPs of the Ami system and comparison with related proteins [Dataset] Alcorlo, Martín Unexpected remarkable promiscuity Streptococcus pneumoniae </ Produced de novo Multiple crystallographic structures Escherichia coli </ Diverse peptide specificities Closed conformations along Certain amino acids >, displaying affinity Ensure sufficient uptake Mass spectrometry analysis div >< p Orchestrating oligopeptide uptake Four proteins building Ami transporter system Abc transporter channel Pneumococci Structural analysis Oligopeptide recognition Oligopeptide binding Uptake mechanism Wide range Vivo implications Transport systems Substantial array Structural basis Silico modelling Shedding light Oligopeptides demonstrates Invasive infections Energy balance Cellular cytoplasm Cell surface Binding cassette Becomes indispensable Auxotrophic nature Abc transporters |
| title_short |
Substrate-binding cavities in OBPs of the Ami system and comparison with related proteins [Dataset] |
| title_full |
Substrate-binding cavities in OBPs of the Ami system and comparison with related proteins [Dataset] |
| title_fullStr |
Substrate-binding cavities in OBPs of the Ami system and comparison with related proteins [Dataset] |
| title_full_unstemmed |
Substrate-binding cavities in OBPs of the Ami system and comparison with related proteins [Dataset] |
| title_sort |
Substrate-binding cavities in OBPs of the Ami system and comparison with related proteins [Dataset] |
| dc.creator.none.fl_str_mv |
Alcorlo, Martín Abdullah, Mohammed R. Steil, Leif Sotomayor, Francisco López de Oro, Laura Castro, Sonia de Velázquez, Sonsoles Kohler, Thomas P. Jiménez, Elisabet Medina, Ana Usón, Isabel Keller, Lance E. Bradshaw, Jessica L. McDaniel, Larry S. Camarasa Rius, María José Völker, Uwe Hammerschmidt, Sven Hermoso, Juan A. |
| author |
Alcorlo, Martín |
| author_facet |
Alcorlo, Martín Abdullah, Mohammed R. Steil, Leif Sotomayor, Francisco López de Oro, Laura Castro, Sonia de Velázquez, Sonsoles Kohler, Thomas P. Jiménez, Elisabet Medina, Ana Usón, Isabel Keller, Lance E. Bradshaw, Jessica L. McDaniel, Larry S. Camarasa Rius, María José Völker, Uwe Hammerschmidt, Sven Hermoso, Juan A. |
| author_role |
author |
| author2 |
Abdullah, Mohammed R. Steil, Leif Sotomayor, Francisco López de Oro, Laura Castro, Sonia de Velázquez, Sonsoles Kohler, Thomas P. Jiménez, Elisabet Medina, Ana Usón, Isabel Keller, Lance E. Bradshaw, Jessica L. McDaniel, Larry S. Camarasa Rius, María José Völker, Uwe Hammerschmidt, Sven Hermoso, Juan A. |
| author2_role |
author author author author author author author author author author author author author author author author author |
| dc.contributor.none.fl_str_mv |
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72] |
| dc.subject.none.fl_str_mv |
Unexpected remarkable promiscuity Streptococcus pneumoniae </ Produced de novo Multiple crystallographic structures Escherichia coli </ Diverse peptide specificities Closed conformations along Certain amino acids >, displaying affinity Ensure sufficient uptake Mass spectrometry analysis div >< p Orchestrating oligopeptide uptake Four proteins building Ami transporter system Abc transporter channel Pneumococci Structural analysis Oligopeptide recognition Oligopeptide binding Uptake mechanism Wide range Vivo implications Transport systems Substantial array Structural basis Silico modelling Shedding light Oligopeptides demonstrates Invasive infections Energy balance Cellular cytoplasm Cell surface Binding cassette Becomes indispensable Auxotrophic nature Abc transporters |
| topic |
Unexpected remarkable promiscuity Streptococcus pneumoniae </ Produced de novo Multiple crystallographic structures Escherichia coli </ Diverse peptide specificities Closed conformations along Certain amino acids >, displaying affinity Ensure sufficient uptake Mass spectrometry analysis div >< p Orchestrating oligopeptide uptake Four proteins building Ami transporter system Abc transporter channel Pneumococci Structural analysis Oligopeptide recognition Oligopeptide binding Uptake mechanism Wide range Vivo implications Transport systems Substantial array Structural basis Silico modelling Shedding light Oligopeptides demonstrates Invasive infections Energy balance Cellular cytoplasm Cell surface Binding cassette Becomes indispensable Auxotrophic nature Abc transporters |
| description |
(A) The bound peptides visualized inside the binding cavity of OBPs belonging to the Ami permease reveal the extent of the unoccupied space. The cavity is shown as a gray semi-transparent surface, the peptide is shown in yellow capped stick, and the protein is not shown. AmiA:5, AmiA in complex with peptide 5; AliD:1, AliD in complex with peptide 1; AliB:2, AliB in complex with peptide 2; AmiB:3, AmiB in complex with peptide 3 and AmiB:4, AmiB in complex with peptide 4. (B) Comparison of the binding cavity volumes found on SBPs of the Ami permease, including the cavities of OppA from L. lactis [PDB 3DRF [30]], AppA from B. subtillis (PDB 1XOC [31]), OppA from S. typhimurium [PDB 1B4Z [26]], DppA [PDB 1DPE] and ProX from E. coli [PDB 1SW2 [33]], for comparative purposes. The volumes were calculated with the program POCASA v1.1 [34] using default parameters and a Probe Radius of 1 Å. |
| publishDate |
2024 |
| dc.date.none.fl_str_mv |
2024 2024 2024 |
| dc.type.none.fl_str_mv |
info:eu-repo/semantics/dataset http://purl.org/coar/resource_type/c_ddb1 Publisher's version info:eu-repo/semantics/publishedVersion |
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dataset |
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publishedVersion |
| dc.identifier.none.fl_str_mv |
http://hdl.handle.net/10261/374492 |
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http://hdl.handle.net/10261/374492 |
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Inglés |
| language_invalid_str_mv |
Inglés |
| dc.relation.none.fl_str_mv |
Alcorlo, Martín; Abdullah, Mohammed R.; Steil, Leif; Sotomayor, Francisco; López de Oro, Laura; Castro, Sonia de ; Velázquez, Sonsoles; Kohler, Thomas P.; Jiménez, Elisabet; Medina, Ana; Usón, Isabel; Keller, Lance E.; Bradshaw, Jessica L..; McDaniel, Larry S.; Camarasa Rius, María José; Völker, Uwe; Hammerschmidt, Sven; Hermoso, Juan A. Molecular and structural basis of oligopeptide recognition by the Ami transporter system in pneumococci. https://doi.org/10.1371/journal.ppat.1011883 . http://hdl.handle.net/10261/364789 https://doi.org/10.1371/journal.ppat.1011883.s024 Sí |
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info:eu-repo/semantics/openAccess |
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openAccess |
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image/tiff |
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Public Library of Science |
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Public Library of Science |
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reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC instname:Consejo Superior de Investigaciones Científicas (CSIC) |
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Consejo Superior de Investigaciones Científicas (CSIC) |
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DIGITAL.CSIC. Repositorio Institucional del CSIC |
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DIGITAL.CSIC. Repositorio Institucional del CSIC |
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1869425492129480704 |
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15,812455 |