6Y16 image
Entry Detail
PDB ID:
6Y16
Title:
CRYSTAL STRUCTURE OF TMARGBP DOMAIN 1 IN COMPLEX WITH THE GUANIDINIUM ION
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2020-02-11
Release Date:
2020-07-15
Method Details:
Experimental Method:
Resolution:
1.70 Å
R-Value Free:
0.18
R-Value Work:
0.16
R-Value Observed:
0.16
Space Group:
P 1
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Amino acid ABC transporter, periplasmic amino acid-binding protein,Amino acid ABC transporter, periplasmic amino acid-binding protein
Chain IDs:A, B
Chain Length:128
Number of Molecules:2
Biological Source:Thermotoga maritima MSB8
Primary Citation
Guanidinium binding to proteins: The intriguing effects on the D1 and D2 domains of Thermotoga maritima Arginine Binding Protein and a comprehensive analysis of the Protein Data Bank.
Int.J.Biol.Macromol. 163 375 385 (2020)
PMID: 32629051 DOI: 10.1016/j.ijbiomac.2020.06.290

Abstact

Thermotoga maritima Arginine Binding Protein has been extensively characterized because of its peculiar features and its possible use as a biosensor. In this characterization, deletion of the C-terminal helix to obtain the monomeric protein TmArgBP20-233 and dissection of the monomer in its two domains, D1 and D2, have been performed. In the present study the stability of these three forms against guanidinium chloride is investigated by means of circular dichroism and differential scanning calorimetry measurements. All three proteins show a high conformational stability; moreover, D1 shows an unusual behavior in the presence of low concentrations of guanidinium chloride. This finding has led us to investigate a possible binding interaction by means of isothermal titration calorimetry and X-ray crystallography; the results indicate that D1 is able to bind the guanidinium ion (GuH+), due to its similarity with the arginine terminal moiety. The analysis of the structural and dynamic properties of the D1-GuH+ complex indicates that the protein binds the ligand through multiple and diversified interactions. An exhaustive survey of the binding modes of GuH+ to proteins indicates that this is a rather common feature. These observations provide interesting insights into the effects that GuH+ is able to induce in protein structures.

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