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...

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Detalles Bibliográficos
Autores: 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.
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
Descripción
Sumario:(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.

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