Crystal structure of the Phe57Trp mutant of the arginine-bound form of domain 1 from TmArgBP

Experimental Data Snapshot

  • Resolution: 1.79 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

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Development of a Protein Scaffold for Arginine Sensing Generated through the Dissection of the Arginine-Binding Protein from Thermotoga maritima .

Smaldone, G.Ruggiero, A.Balasco, N.Vitagliano, L.

(2020) Int J Mol Sci 21

  • DOI: https://doi.org/10.3390/ijms21207503
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Arginine is one of the most important nutrients of living organisms as it plays a major role in important biological pathways. However, the accumulation of arginine as consequence of metabolic defects causes hyperargininemia, an autosomal recessive disorder. Therefore, the efficient detection of the arginine is a field of relevant biomedical/biotechnological interest. Here, we developed protein variants suitable for arginine sensing by mutating and dissecting the multimeric and multidomain structure of Thermotoga maritima arginine-binding protein (TmArgBP). Indeed, previous studies have shown that TmArgBP domain-swapped structure can be manipulated to generate simplified monomeric and single domain scaffolds. On both these stable scaffolds, to measure tryptophan fluorescence variations associated with the arginine binding, a Phe residue of the ligand binding pocket was mutated to Trp. Upon arginine binding, both mutants displayed a clear variation of the Trp fluorescence. Notably, the single domain scaffold variant exhibited a good affinity (~3 µM) for the ligand. Moreover, the arginine binding to this variant could be easily reverted under very mild conditions. Atomic-level data on the recognition process between the scaffold and the arginine were obtained through the determination of the crystal structure of the adduct. Collectively, present data indicate that TmArgBP scaffolds represent promising candidates for developing arginine biosensors.

  • Organizational Affiliation

    IRCCS SDN, Via Emanuele Gianturco, 113 80143 Naples, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Amino acid ABC transporter, periplasmic amino acid-binding protein,Amino acid ABC transporter, periplasmic amino acid-binding protein
A, B
136Thermotoga maritimaThermotoga maritima MSB8
This entity is chimeric
Mutation(s): 1 
Gene Names: TM_0593
Find proteins for Q9WZ62 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8))
Explore Q9WZ62 
Go to UniProtKB:  Q9WZ62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9WZ62
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.79 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.48α = 90
b = 67.217β = 90
c = 102.411γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-04
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Database references, Refinement description