6GPD

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

Summary for 6GPD

• Entry DOI: 10.2210/pdb6gpd/pdb
• Descriptor: Amino acid ABC transporter, periplasmic amino acid-binding protein,Amino acid ABC transporter, periplasmic amino acid-binding protein (2 entities in total)
• Functional Keywords: domain-domain communication, diagnostic tool, protein dissection, biosensor, protein structure-stability, transport protein
• Biological source: Thermotoga maritima MSB8; More
• Total number of polymer chains: 2
• Total formula weight: 27715.57

Authors

Smaldone, G.,Balasco, N.,Ruggiero, A.,Berisio, R.,Vitagliano, L. (deposition date: 2018-06-05, release date: 2018-08-15, Last modification date: 2024-01-17)

Primary citation

Smaldone, G.,Balasco, N.,Vigorita, M.,Ruggiero, A.,Cozzolino, S.,Berisio, R.,Del Vecchio, P.,Graziano, G.,Vitagliano, L.
Domain communication in Thermotoga maritima Arginine Binding Protein unraveled through protein dissection.
Int. J. Biol. Macromol., 119:758-769, 2018

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.

PubMed: 30059738
DOI: 10.1016/j.ijbiomac.2018.07.172

Experimental method

X-RAY DIFFRACTION (1.75 Å)