PDBsum entry 5ipw

Peptide binding protein

PDB id: 5ipw

Contents

Protein chain

633 a.a.

Waters ×155

PDB id:

5ipw

Name:

Peptide binding protein

Title:

Oligopeptide-binding protein oppa

Structure:

Oligopeptide abc transporter, periplasmic oligopeptide- binding protein, putative. Chain: a. Fragment: unp residues 31-659. Engineered: yes

Source:

Thermotoga maritima msb8. Organism_taxid: 243274. Strain: msb8. Gene: tm_0056. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.60Å R-factor: 0.211 R-free: 0.239

Authors:

H.H.Lee,H.J.Kim,H.J.Yoon

Key ref:

H.J.Yoon et al. (2016). Crystal structure of a putative oligopeptide-binding periplasmic protein from a hyperthermophile. Extremophiles, 20, 723-731. PubMed id: 27377296 DOI: 10.1007/s00792-016-0861-7

Date:

10-Mar-16 Release date: 15-Mar-17

Protein chain

Q9WXR2  (Q9WXR2_THEMA) -  Oligopeptide ABC transporter, periplasmic oligopeptide-binding protein, putative from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)

Seq: 660 a.a.

Struc: 633 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1007/s00792-016-0861-7

Extremophiles 20:723-731 (2016)

PubMed id: 27377296

Crystal structure of a putative oligopeptide-binding periplasmic protein from a hyperthermophile.

H.J.Yoon, H.J.Kim, B.Mikami, Y.G.Yu, H.H.Lee.

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.