8UPI | pdb_00008upi

Structure of a periplasmic peptide binding protein from Mesorhizobium sp. AP09 bound to aminoserine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.229 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.181 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 

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Literature

Identification and Characterization of a Bacterial Periplasmic Solute Binding Protein That Binds l-Amino Acid Amides.

Smith, O.B.Frkic, R.L.Rahman, M.G.Jackson, C.J.Kaczmarski, J.A.

(2024) Biochemistry 63: 1322-1334

  • DOI: https://doi.org/10.1021/acs.biochem.4c00096
  • Primary Citation of Related Structures:  
    8UPI

  • PubMed Abstract: 

    Periplasmic solute-binding proteins (SBPs) are key ligand recognition components of bacterial ATP-binding cassette (ABC) transporters that allow bacteria to import nutrients and metabolic precursors from the environment. Periplasmic SBPs comprise a large and diverse family of proteins, of which only a small number have been empirically characterized. In this work, we identify a set of 610 unique uncharacterized proteins within the SBP_bac_5 family that are found in conserved operons comprising genes encoding (i) ABC transport systems and (ii) putative amidases from the FmdA_AmdA family. From these uncharacterized SBP_bac_5 proteins, we characterize a representative periplasmic SBP from Mesorhizobium sp. A09 ( Me Ami_SBP) and show that Me Ami_SBP binds l-amino acid amides but not the corresponding l-amino acids. An X-ray crystal structure of Me Ami_SBP bound to l-serinamide highlights the residues that impart distinct specificity for l-amino acid amides and reveals a structural Ca 2+ binding site within one of the lobes of the protein. We show that the residues involved in ligand and Ca 2+ binding are conserved among the 610 SBPs from experimentally uncharacterized FmdA_AmdA amidase-associated ABC transporter systems, suggesting these homologous systems are also likely to be involved in the sensing, uptake, and metabolism of l-amino acid amides across many Gram-negative nitrogen-fixing soil bacteria. We propose that Me Ami_SBP is involved in the uptake of such solutes to supplement pathways such as the citric acid cycle and the glutamine synthetase-glutamate synthase pathway. This work expands our currently limited understanding of microbial interactions with l-amino acid amides and bacterial nitrogen utilization.


  • Organizational Affiliation

    Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 2601, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptide ABC transporter substrate-binding protein523Mesorhizobium sp. AP09Mutation(s): 0 
Gene Names: MesoLj113b_06930
UniProt
Find proteins for A0A7R6WUD2 (Mesorhizobium sp. 113-3-3)
Explore A0A7R6WUD2 
Go to UniProtKB:  A0A7R6WUD2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7R6WUD2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.229 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.181 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.247α = 90
b = 58.92β = 90
c = 139.355γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
CrysalisProdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SETClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaCE200100029

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-08
    Type: Initial release
  • Version 1.1: 2024-05-22
    Changes: Database references
  • Version 1.2: 2024-06-05
    Changes: Database references
  • Version 1.3: 2024-10-23
    Changes: Structure summary