6Y16

CRYSTAL STRUCTURE OF TMARGBP DOMAIN 1 IN COMPLEX WITH THE GUANIDINIUM ION

Summary for 6Y16

• Entry DOI: 10.2210/pdb6y16/pdb
• Related: 6GPC
• Descriptor: Amino acid ABC transporter, periplasmic amino acid-binding protein,Amino acid ABC transporter, periplasmic amino acid-binding protein, GUANIDINE, 1,2-ETHANEDIOL, ... (4 entities in total)
• Functional Keywords: complex, transport protein
• Biological source: Thermotoga maritima MSB8; More
• Total number of polymer chains: 2
• Total formula weight: 28478.60

Authors

Ruggiero, A.,Balasco, N.,Smaldone, G.,Graziano, G.,Vitagliano, L. (deposition date: 2020-02-11, release date: 2020-07-15, Last modification date: 2024-01-24)

Primary citation

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

PubMed Abstract: 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 TmArgBP 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.

PubMed: 32629051
DOI: 10.1016/j.ijbiomac.2020.06.290

Experimental method

X-RAY DIFFRACTION (1.7 Å)