PDBsum entry 3efc

Membrane protein

PDB id: 3efc

Contents

Protein chain

327 a.a. *

* Residue conservation analysis

PDB id:

3efc

Name:

Membrane protein

Title:

Crystal structure of yaet periplasmic domain

Structure:

Outer membrane protein assembly factor yaet. Chain: a. Fragment: periplasmic domain (unp residues 21-410). Synonym: omp85. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Gene: yaet, yzzn, yzzy, b0177, jw0172. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

3.30Å R-factor: 0.267 R-free: 0.295

Authors:

P.Z.Gatzeva-Topalova,T.A.Walton,M.C.Sousa

Key ref:

P.Z.Gatzeva-Topalova et al. (2008). Crystal structure of YaeT: conformational flexibility and substrate recognition. Structure, 16, 1873-1881. PubMed id: 19081063 DOI: 10.1016/j.str.2008.09.014

Date:

08-Sep-08 Release date: 16-Dec-08

Protein chain

P0A940  (BAMA_ECOLI) -  Outer membrane protein assembly factor BamA from Escherichia coli (strain K12)

Seq: 810 a.a.

Struc: 327 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1016/j.str.2008.09.014

Structure 16:1873-1881 (2008)

PubMed id: 19081063

Crystal structure of YaeT: conformational flexibility and substrate recognition.

P.Z.Gatzeva-Topalova, T.A.Walton, M.C.Sousa.

ABSTRACT

The envelope of Gram-negative bacteria consists of inner and outer membranes surrounding the peptidoglycan wall. The outer membrane (OM) is rich in integral membrane proteins (OMPs), which have a characteristic beta barrel domain embedded in the OM. The Omp85 family of proteins, ubiquitous among Gram-negative bacteria and also present in chloroplasts and mitochondria, is required for folding and insertion of OMPs into the outer membrane. Bacterial Omp85 proteins are characterized by a periplasmic domain containing five repeats of polypeptide transport-associated (POTRA) motifs. Here we report the crystal structure of a periplasmic fragment of YaeT (the Escherichia coli Omp85) containing the first four POTRA domains in an extended conformation consistent with recent solution X-ray scattering data. Analysis of the YaeT structure reveals conformational flexibility around a hinge point between POTRA2 and 3 domains. The structure's implications for substrate binding and folding mechanisms are also discussed.

Selected figure(s)

Figure 2.
Figure 2. Conformational Flexibility of the YaeT Periplasmic Domain
(A and B) Superposition of the structure of YaeT[21:359] presented here with that of YaeT[21:351] determined by Kim et al. (2007) (Protein Data Bank [PDB] ID code 2QDF). The two structures are superimposed on POTRA1 and 2 (A) or POTRA3 and 4 (B). The color scheme for YaeT[21:359] is the same as in Figure 1. The color scheme for Kim et al.'s structure is as follows: POTRA1, magenta; POTRA2, blue; POTRA3, dark green; POTRA4, raspberry.
(C–E) Interfaces between POTRA domains 1 and 2 (C), 2 and 3 (D), and 3 and 4 (E). Interacting residues are shown as sticks and secondary structure elements are shown in cartoon representation. A semitransparent surface representation is shown to highlight the extent of surface interaction between the domains.

Figure 5.
Figure 5. Comparison of the Structures of YaeT POTRA3 and SecB
(A and B) Cartoon representations of SecB (PDB ID code 1FX3) (A) and YaeT POTRA3 (B). Aromatic residues lining the top of a hydrophobic groove (Subsite1) are highlighted in brown-red. Hydrophobic (but not aromatic) residues forming an extended hydrophobic groove (Subsite2) are shown in light magenta.

The above figures are reprinted from an Open Access publication published by Cell Press: Structure (2008, 16, 1873-1881) copyright 2008.

Figures were selected by an automated process.