3QKY

Crystal structure of Rhodothermus marinus BamD

Summary for 3QKY

• Entry DOI: 10.2210/pdb3qky/pdb
• Descriptor: Outer membrane assembly lipoprotein YfiO (2 entities in total)
• Functional Keywords: outer membrane, membrane protein
• Biological source: Rhodothermus marinus (Rhodothermus obamensis)
• Total number of polymer chains: 1
• Total formula weight: 30879.48

Authors

Sandoval, C.M.,Baker, S.L.,Jansen, K.,Metzner, S.I.,Sousa, M.C. (deposition date: 2011-02-02, release date: 2011-04-20, Last modification date: 2024-05-22)

Primary citation

Sandoval, C.M.,Baker, S.L.,Jansen, K.,Metzner, S.I.,Sousa, M.C.
Crystal structure of BamD: an essential component of the beta-Barrel assembly machinery of gram-negative bacteria.
J.Mol.Biol., 409:348-357, 2011

PubMed Abstract: Folding and insertion of integral β-barrel proteins in the outer membrane (OM) is an essential process for Gram-negative bacteria that requires the β-barrel assembly machinery (BAM). Efficient OM protein (OMP) folding and insertion appears to require a consensus C-terminal signal in OMPs characterized by terminal F or W residues. The BAM complex is embedded in the OM and, in Escherichia coli, consists of the β-barrel BamA and four lipoproteins BamBCDE. BamA and BamD are broadly distributed across all species of Gram-negative bacteria, whereas the other components are present in only a subset of species. BamA and BamD are also essential for viability, suggesting that these two proteins constitute the functional core of the bacterial BAM complex. Here, we present the crystal structure of BamD from the thermophilic bacteria Rhodothermus marinus refined to 2.15 Å resolution. The protein contains five tetratricopeptide repeats (TPRs) organized into two offset tandems, each capped by a terminal helix. The N-terminal domain contains three TPRs and displays remarkable structural similarity with proteins that recognize targeting signals in extended conformations. The C-terminal domain harbors the remaining two TPRs and previously described mutations that impair binding to other BAM components map to this domain. Therefore, the structure suggests a model where the C-terminal domain provides a scaffold for interaction with BAM components, while the N-terminal domain participates in interaction with the substrates, either recognizing the C-terminal consensus sequence or binding unfolded OMP intermediates.

PubMed: 21463635
DOI: 10.1016/j.jmb.2011.03.035

Experimental method

X-RAY DIFFRACTION (2.15 Å)