PDBsum entry 1orm

Membrane protein

PDB id: 1orm

Contents

Protein chain

148 a.a. *

* Residue conservation analysis

PDB id:

1orm

Name:

Membrane protein

Title:

Nmr fold of the outer membrane protein ompx in dhpc micelles

Structure:

Outer membrane protein x. Chain: a. Synonym: outer membrane protein ompx. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: ompx. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

20 models

Authors:

C.Fernandez,K.Adeishvili,K.Wuthrich

Key ref:

C.Fernández et al. (2001). Transverse relaxation-optimized NMR spectroscopy with the outer membrane protein OmpX in dihexanoyl phosphatidylcholine micelles. Proc Natl Acad Sci U S A, 98, 2358-2363. PubMed id: 11226244 DOI: 10.1073/pnas.051629298

Date:

14-Mar-03 Release date: 22-Apr-03

Protein chain

P0A917  (OMPX_ECOLI) -  Outer membrane protein X from Escherichia coli (strain K12)

Seq: 171 a.a.

Struc: 148 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1073/pnas.051629298

Proc Natl Acad Sci U S A 98:2358-2363 (2001)

PubMed id: 11226244

Transverse relaxation-optimized NMR spectroscopy with the outer membrane protein OmpX in dihexanoyl phosphatidylcholine micelles.

C.Fernández, K.Adeishvili, K.Wüthrich.

ABSTRACT

The (2)H,(13)C,(15)N-labeled, 148-residue integral membrane protein OmpX from Escherichia coli was reconstituted with dihexanoyl phosphatidylcholine (DHPC) in mixed micelles of molecular mass of about 60 kDa. Transverse relaxation-optimized spectroscopy (TROSY)-type triple resonance NMR experiments and TROSY-type nuclear Overhauser enhancement spectra were recorded in 2 mM aqueous solutions of these mixed micelles at pH 6.8 and 30 degrees C. Complete sequence-specific NMR assignments for the polypeptide backbone thus have been obtained. The (13)C chemical shifts and the nuclear Overhauser effect data then resulted in the identification of the regular secondary structure elements of OmpX/DHPC in solution and in the collection of an input of conformational constraints for the computation of the global fold of the protein. The same type of polypeptide backbone fold is observed in the presently determined solution structure and the previously reported crystal structure of OmpX determined in the presence of the detergent n-octyltetraoxyethylene. Further structure refinement will have to rely on the additional resonance assignment of partially or fully protonated amino acid side chains, but the present data already demonstrate that relaxation-optimized NMR techniques open novel avenues for studies of structure and function of integral membrane proteins.

Selected figure(s)

Figure 3.
Fig. 3. (a) Survey of the NMR assignments for OmpX/DHPC obtained by TROSY-type triple-resonance experiments. The residues for which the 1HN, 15N, 13C^ , 13C^ , and 13CO chemical shifts have been assigned are indicated by vertical bars in the respective rows. In the center, separating a and b, the amino acid sequence is indicated by the one-letter amino acid symbols, where the entries have been distributed over two rows, i.e., residue 1 is in the upper row, residue 2 is in the lower row, etc. (b) Plot of ( C^ C^ ) vs. the amino acid sequence. C^ and C^ were obtained as the differences between the experimental 13C^ and 13C^ chemical shifts in OmpX/DHPC and the corresponding random coil shifts. The value of ( C^ C^ ) for a particular residue i represents the average over the three consecutive residues i 1, i and i + 1, and was calculated as follows: - DC^b)_i = 1/3(DC_{i -1}^a + DC_i^a + DC_i+1^a - DC_{i -1}^b - DC_i^b - DC_i+1^b) (41). Negative values of ( C^ C^ ) indicate that residue i is located in a regular -strand (positive values would indicate location in a regular helical structure). The positions of the regular secondary structure elements in the crystal structure of OmpX are indicated at the top, and the external loops (L) and periplasmatic turns (T) are labeled according to Vogt and Schulz (23).

Figure 5.
Fig. 5. Stereoviews of the polypeptide backbone fold in OmpX. (a) Superposition of the 20 DYANA conformers that were selected to represent the NMR structure of OmpX. The superposition is for pairwise global best fit of the N, C^ , and C' backbone atoms of the -sheet amino acid residues in conformers 2-20 with the corresponding atoms in the conformer with the smallest residual target function value (Table 1). (b) Comparison of the mean NMR structure (blue) and the x-ray crystal structure (red) after superposition as in a. Periplasmatic and extracellular spaces are indicated according to ref. 23. The figure was prepared with the program MOLMOL (43).

Figures were selected by an automated process.