The crystal structure of BamB suggests interactions with BamA and its role within the BAM complex - PubMed (original) (raw)

The crystal structure of BamB suggests interactions with BamA and its role within the BAM complex

Nicholas Noinaj et al. J Mol Biol. 2011.

Abstract

Escherichia coli BamB is the largest of four lipoproteins in the β-barrel assembly machinery (BAM) complex. It interacts with the periplasmic domain of BamA, an integral outer membrane protein (OMP) essential for OMP biogenesis. Although BamB is not essential, it serves an important function in the BAM complex, significantly increasing the folding efficiency of some OMPs in vivo and in vitro. To learn more about the BAM complex, we solved structures of BamB in three different crystal forms. BamB crystallized in space groups P2(1)3, I222, and P2(1)2(1)2(1), with one molecule per asymmetric unit in each case. Crystals from the space group I222 diffracted to 1. 65-Å resolution. BamB forms an eight-bladed β-propeller with a central pore and is shaped like a doughnut. A DALI search revealed that BamB shares structural homology to several eukaryotic proteins containing WD40 repeat domains, which commonly have β-propeller folds and often serve as scaffolding proteins within larger multi-protein complexes that carry out signal transduction, cell division, and chemotaxis. Using mutagenesis data from previous studies, we docked BamB onto a BamA structural model and assessed known and possible interactions between these two proteins. Our data suggest that BamB serves as a scaffolding protein within the BAM complex by optimally orienting the flexible periplasmic domain of BamA for interaction with other BAM components and chaperones. This may facilitate integration of newly synthesized OMPs into the outer membrane.

Published by Elsevier Ltd.

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Figures

Figure 1

Figure 1

Overall structure of BamB. A, BamB has an eight bladed β-propeller fold with each blade shown in a different color (N-terminal residues 21–40 have been removed for clarity) and is rotated 90° about the x-axis in panel B. C, Space-filling representation of BamB rendered transparent and rotated 90° about the x-axis in panel D.

Figure 2

Figure 2

Surface characteristics of BamB. A, Electrostatic surface potential representation of BamB shows that the core region is strongly electronegative on both sides (B and C, rotated +90° and −90° about x-axis compared to panel A, respectively, to illustrate both sides). D. Surface hydrophobicity of BamB highlighting the most hydrophobic residues in yellow. The locations of IL2, IL4, and IL5 are indicated for reference.

Figure 3

Figure 3

BamB IL4 and IL5 are partially disordered and contain residues important for binding BamA. A, B-factor putty representation of BamB (P213) shows that the structure is mostly ordered with only N-terminal residues 21–40, IL4, and IL5 showing significant flexibility. B, Zoomed view indicating residues in BamB that were previously shown to lie within the binding interface with BamA. BamB is color coded according to Figure 1, important residues are shown in stick representation, and the disordered residues in IL5 are represented by a dashed line.

Figure 4

Figure 4

Sequence alignment of BamB homologs from Escherichia coli (EcBamB), Pseudomonas aeruginosa (PaBamB), and Vibrio cholerae (VcBamB). A, Residues having a conservation score of 7.5 or greater are color coded from yellow (7.5) to blue (11, max) and mapped onto the surface of the BamB structure. The BamB secondary structure is shown above the sequence alignment. Residues that have previously been reported to be involved in binding BamA are indicated by red asterisks. B, Conserved residues (blue) having a conservation score of 7.5 or greater were mapped onto the BamB crystal structure reported here.

Figure 5

Figure 5

BamB shows structural similarity to proteins containing WD40 repeat-like domains. A, β-propeller blade 2 from the BamB crystal structure (stick model) showing the electron density (blue mesh) from a σ– A weighted 2Fo-Fc map contoured at 1.0 σ. B, Ribbon representation of blade 2 illustrating its WD40 repeat-like domain structure, showing tryptophan and aspartate residues in stick representation. C, Ribbon representation of a WD40 repeat domain from Cdc41, showing tryptophan and aspartate residues in stick representation. D, Superposition of the WD40 domain from Cdc41 and the WD40 repeat-like domain from BamB.

Figure 6

Figure 6

Docking the BamA-BamB complex. A, Docked structure of BamB (green) onto POTRA 1-5, with each of the POTRA domains shown in a different color and in panel B, rotated 90° along the y-axis. C, Electrostatic charge distributions for POTRA 1-4, with BamB shown in green. D, Zoomed view of docked structure along POTRA 2-4, highlighting residues in IL4 (blue) and IL5 (pink) important for binding and a potential salt bridge formed between D241 (BamA) and R195 (BamB). As predicted from previous reports and obtained as a result in our docked model, strand β2 from POTRA 3 appears to interact with BamB IL4 (blue) by β-strand augmentation.

Figure 7

Figure 7

Model depicting how BamB interacts with BamA at the outer membrane. This model is based upon previously reported studies, homology to known structures, and our docking studies with the BamB structures.

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