5IPW

oligopeptide-binding protein OppA

Summary for 5IPW

• Entry DOI: 10.2210/pdb5ipw/pdb
• Descriptor: Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein, putative (2 entities in total)
• Functional Keywords: oligopeptide-binding protein, peptide binding protein
• Biological source: Thermotoga maritima MSB8
• Total number of polymer chains: 1
• Total formula weight: 72971.51

Authors

Lee, H.H.,Kim, H.J.,Yoon, H.J. (deposition date: 2016-03-10, release date: 2017-03-15, Last modification date: 2024-03-20)

Primary citation

Yoon, H.J.,Kim, H.J.,Mikami, B.,Yu, Y.G.,Lee, H.H.
Crystal structure of a putative oligopeptide-binding periplasmic protein from a hyperthermophile
Extremophiles, 20:723-731, 2016

PubMed Abstract: Oligopeptide-binding proteins (Opps) are part of the ATP-binding cassette system, playing a crucial role in nutrient uptake and sensing the external environment in bacteria, including hyperthermophiles. Opps serve as a binding platform for diverse peptides; however, how these peptides are recognized by Opps is still largely unknown and few crystal structures of Opps from hyperthermophiles have been determined. To facilitate such an understanding, the crystal structure of a putative Opp, OppA from Thermotoga maritima (TmOppA), was solved at 2.6-Å resolution in the open conformation. TmOppA is composed of three domains. The N-terminal domain consists of twelve strands, nine helices, and four 310 helices, and the C-terminal domain consists of five strands, ten helices, and one 310 helix. These two domains are connected by the linker domain, which consists of two strands, three helices, and three 310 helices. Based on structural comparisons of TmOppA with other OppAs and binding studies, we suggest that TmOppA might be a periplasmic Opp. The most distinct feature of TmOppA is the insertion of two helices, which are lacking in other OppAs. A cavity volume between the N-terminal and C-terminal domains is suggested to be responsible for binding peptides of various lengths.

PubMed: 27377296
DOI: 10.1007/s00792-016-0861-7

Experimental method

X-RAY DIFFRACTION (2.6 Å)