Crystal structure of the ligand-free form of domain 1 from TmArgBP

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

Starting Model: experimental
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Domain communication in Thermotoga maritima Arginine Binding Protein unraveled through protein dissection.

Smaldone, G.Balasco, N.Vigorita, M.Ruggiero, A.Cozzolino, S.Berisio, R.Del Vecchio, P.Graziano, G.Vitagliano, L.

(2018) Int J Biol Macromol 119: 758-769

  • DOI: https://doi.org/10.1016/j.ijbiomac.2018.07.172
  • Primary Citation of Related Structures:  
    6GPC, 6GPD, 6GPM

  • PubMed Abstract: 

    Substrate binding proteins represent a large protein family that plays fundamental roles in selective transportation of metabolites across membrane. The function of these proteins relies on the relative motions of their two domains. Insights into domain communication in this class of proteins have been here collected using Thermotoga maritima Arginine Binding Protein (TmArgBP) as model system. TmArgBP was dissected into two domains (D1 and D2) that were exhaustively characterized using a repertoire of different experimental and computational techniques. Indeed, stability, crystalline structure, ability to recognize the arginine substrate, and dynamics of the two individual domains have been here studied. Present data demonstrate that, although in the parent protein both D1 and D2 cooperate for the arginine anchoring; only D1 is intrinsically able to bind the substrate. The implications of this finding on the mechanism of arginine binding and release by TmArgBP have been discussed. Interestingly, both D1 and D2 retain the remarkable thermal/chemical stability of the parent protein. The analysis of the structural and dynamic properties of TmArgBP and of the individual domains highlights possible routes of domain communication. Finally, this study generated two interesting molecular tools, the two stable isolated domains that could be used in future investigations.

  • Organizational Affiliation

    IRCCS SDN, Via Emanuele Gianturco 113, 80143 Napoli, Italy. Electronic address: gsmaldone@sdn-napoli.it.

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
126Thermotoga maritima MSB8Mutation(s): 0 
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: 1.75 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.445α = 116.01
b = 46.036β = 109.85
c = 52.496γ = 90.01
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description