Structural basis for lipopolysaccharide extraction by abc transporter lptb2fg

ABSTRACT After biosynthesis, bacterial lipopolysaccharides (LPS) are transiently anchored to the outer leaflet of the inner membrane (IM). The ATP-binding cassette (ABC) transporter LptB2FG

extracts LPS molecules from the IM and transports them to the outer membrane. Here we report the crystal structure of nucleotide-free LptB2FG from _Pseudomonas aeruginosa_. The structure

reveals that lipopolysaccharide transport proteins LptF and LptG each contain a transmembrane domain (TMD), a periplasmic β-jellyroll-like domain and a coupling helix that interacts with

LptB on the cytoplasmic side. The LptF and LptG TMDs form a large outward-facing V-shaped cavity in the IM. Mutational analyses suggest that LPS may enter the central cavity laterally, via

the interface of the TMD domains of LptF and LptG, and is expelled into the β-jellyroll-like domains upon ATP binding and hydrolysis by LptB. These studies suggest a mechanism for LPS

extraction by LptB2FG that is distinct from those of classical ABC transporters that transport substrates across the IM. Access through your institution Buy or subscribe This is a preview of

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Chemical Society_ 238 (ACS, 2009). Download references ACKNOWLEDGEMENTS The authors thank Z. Liu, X. Zhang and H. Wu for valuable discussions and critically reading the manuscript. The

authors also thank N. Ruiz (Department of Microbiology, The Ohio State University, Columbus, Ohio, USA) for generously providing the _lptFG_-depleted NR1113 _E. coli_ strain. The diffraction

data were collected at the Shanghai Synchrotron Radiation Facility (SSRF, China) and National Center for Protein Science Shanghai (NCPSS, China). This work was supported by grants from the

National Natural Science Foundation of China (31625009 to Y.H.), the Ministry of Science and Technology (2016YFA0500404 and 2013CB910603 to Y.H.) and the Strategic Priority Research Program

of the Chinese Academy of Sciences (XDB08020302 to Y. H.). AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * National Laboratory of Biomacromolecules, CAS Center for Excellence in

Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China Qingshan Luo, Xu Yang, Shan Yu, Huigang Shi, Le Xiao, Chuanqi Sun, Xinzheng Zhang & Yihua Huang *

University of Chinese Academy of Sciences, Beijing, China Qingshan Luo, Huigang Shi, Le Xiao, Chuanqi Sun, Xinzheng Zhang & Yihua Huang * Institute of Bio-analytical Chemistry, School of

Chemical Engineering, Nanjing University of Science and Technology, Nanjing, P.R.China Kun Wang & Min Zhou * Discovery Biology, Albany Molecular Research Inc., Buffalo, New York, USA

Guangyu Zhu * National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological

Sciences, Chinese Academy of Sciences, Shanghai, China Tingting Li & Dianfan Li Authors * Qingshan Luo View author publications You can also search for this author inPubMed Google

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Scholar * Huigang Shi View author publications You can also search for this author inPubMed Google Scholar * Kun Wang View author publications You can also search for this author inPubMed 

Google Scholar * Le Xiao View author publications You can also search for this author inPubMed Google Scholar * Guangyu Zhu View author publications You can also search for this author

inPubMed Google Scholar * Chuanqi Sun View author publications You can also search for this author inPubMed Google Scholar * Tingting Li View author publications You can also search for this

author inPubMed Google Scholar * Dianfan Li View author publications You can also search for this author inPubMed Google Scholar * Xinzheng Zhang View author publications You can also

search for this author inPubMed Google Scholar * Min Zhou View author publications You can also search for this author inPubMed Google Scholar * Yihua Huang View author publications You can

also search for this author inPubMed Google Scholar CONTRIBUTIONS Y.H. supervised the project. Q.L., X.Y., S.Y., H.S., K.W., L.X. and T.L. performed the experiments. Q.L. and Y.H. collected

diffraction data. Y.H., Q.L. and G.Z. built the model and refined the structure. Y.H., C.S., G.Z., X.Z., D.L. and M.Z. contributed to manuscript preparation. Y.H. and Q.L. wrote the

manuscript. All authors contributed to data analysis. CORRESPONDING AUTHOR Correspondence to Yihua Huang. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing financial

interests. INTEGRATED SUPPLEMENTARY INFORMATION SUPPLEMENTARY FIGURE 1 CHEMICAL STRUCTURE OF LPS AND LPS BIOGENESIS IN GRAM-NEGATIVE BACTERIA. A. Chemical structure of LPS. LPS molecule

consists of Lipid A, core oligosaccharide and O-antigen. The polar part of Lipid A is negatively-changed due to the presence of two phosphate groups. B. Ra-LPS molecule is approximately 32Å

in height and 28 Å×12 Å in the other two dimensions. The dimensions of an Ra-LPS is based on the crystal structure of TLR4/MD-2/Ra-LPS complex (PDB ID: 3FXI). C. LPS biogenesis in

Gram-negative bacteria. After flipped to the IM outer leaflet by MsbA, LPS is extracted from IM, transported cross the periplasm and finally inserted in the OM by the LptABCDEFG

transenvelope complex. LptB2FG is a quaternary ABC transporter. SUPPLEMENTARY FIGURE 2 THE ELECTRON DENSITY MAPS OF LPTB2FG. A. Stereo views (cross-eyed) of the 2Fo-Fc electron density map

for the complete LptB2FG complex structure at 3.46Å. B. The 2Fo-Fc electron density maps of representative regions of the TMDs of LptFG (TM1-LptF and TM1-LptG) are shown. Selenomethionine

residues (in red) and bulky residues are used as makers for guiding model building. C-D. Validation of side-chain register of the nucleotide-free LptB2FG transporter. Anomalous electron

density maps define selenomethionine (contour level: 3.0σ) in (C) and Pt sites (contour level: 4.5σ) in (D). In (C), anomalous density was observed for 28 out of 32 selenomethionines of the

complete LptB2FG complex. SUPPLEMENTARY FIGURE 3 DOMAIN ORGANIZATION OF THE LPTB2FG COMPLEX. A. Domain organization of the LptB2FG complex. The two ATPase domains (LptB) in cytoplasm are

colored in cyan and green. The TMD domains of LptF and LptG, each containing six transmembrane helices, are colored in violet and yellow, respectively. The two periplasmic β-jellyroll

domains of LptF and LptG that stem from TM3 and TM4 of LptF(G) are colored in grey. The two coupling helices of LptF and LptG connecting TM2 and TM3 of LptF(G) in cytoplasm are highlighted

in blue. B. Overlay of the TMD of LptF with that of LptG. LptF and LptG are colored in violet and yellow, respectively. SUPPLEMENTARY FIGURE 4 SEQUENCE ALIGNMENT OF LPTF HOMOLOGS AND

RESIDUES SELECTED FOR FUNCTIONAL ANALYSIS IN THE STRUCTURE. A. Sequence alignment of LptF homologs from five representative Gram-negative bacterial strains. B. Conserved hydrophobic and

positive residues of LptF lining the “V”-shaped cavity selected for mutational studies. Conservation of LptF residues in different Gram-negative homologs is shown in ENDscript. Secondary

structures are numbered within the respective domains. Conserved residues lining the inner surface of the “V”-shaped cavity were selected for mutational analyses are highlighted. The labeled

residue types and numbers in both alignments correspond to those in _E. coli_. SUPPLEMENTARY FIGURE 5 SEQUENCE ALIGNMENT OF LPTG HOMOLOGS AND RESIDUES SELECTED FOR FUNCTIONAL ANALYSIS IN

THE STRUCTURE. A. Sequence alignment of LptG homologs from five representative Gram-negative bacterial strains. B. Conserved hydrophobic and positive residues of LptG lining the “V”-shaped

cavity selected for mutational studies. Conservation of LptG residues in different Gram-negative homologs is shown in ENDscript. Secondary structures are numbered within the respective

domains. Conserved residues lining the inner surface of the “V”-shaped cavity were selected for mutational analyses are highlighted. The labeled residue types and numbers in both alignments

correspond to those in _E. coli_. SUPPLEMENTARY FIGURE 6 MUTAGENESIS STUDY OF THE CONSERVED RESIDUES THAT LINE THE INNER SURFACE OF THE “V”-SHAPED CAVITY IN THE TMDS OF LPTF AND LPTG. The

growth phenotypes of the _lptFG_-depleted _E. coli_ strain NR1113 transformed with various hydrophobic-to-hydrophilic LptG_Ec mutants (A) and LptF_Ec mutants (B) on LB agar plates containing

0.1% L-arabinose and 50 μg ml−1 kanamycin. The growth phenotypes of the _lptFG_-depleted _E. coli_ strain NR1113 transformed with positive-to-negative mutations in the absence of

L-aribinose (C), mutant protein expression levels (D) and the growth phenotypes in the presence of 0.1% L-arabinose (E). Mutational analyses of residues from the coupling helices of LptF_Ec

and LptG_Ec on LB agar plates containing 0.1% L-arabinose and 50 μg ml−1 kanamycin (F). All labeled residue types and numbers correspond to those of LptF_Ec and LptG_Ec. In the presence of

0.1% L-arabinose, the _lptFG_-depleted _E. coli_ strain NR1113 transformed with WT, vector control and various mutants all grew well similar to that of WT. In the absence of L-arabinose, the

_lptFG_-depleted _E. coli_ strain NR1113 transformed with pQLink-Kan vector and plasmids encoding wild-type (WT) LptFG were used as negative control and positive control, respectively. All

the complementation assays were repeated at least three times and a representative result is shown. SUPPLEMENTARY FIGURE 7 THREE REPRESENTATIVE ABC EXPORTERS IN THEIR INWARD-FACING OR

OUTWARD-FACING CONFORMATIONAL STATES. The nucleotide-free LptB2FG transporter (A), the heterodimeric TM287-TM288 exporter in the apo state (PDB code: 4Q4H) (B) and the heterodimeric

nucleotide-free human sterol ABCG5-ABCG8 exporter (PDB code: 5DO7) (C) in inward-facing conformational state; the homodimeric AMP-PNP-bound Sav1866 exporter (PDB code: 2ONJ) (D) in

outward-facing conformational state. SUPPLEMENTARY INFORMATION SUPPLEMENTARY TEXT AND FIGURES Supplementary Figures 1–7 (PDF 1557 kb) SUPPLEMENTARY DATA SET 1 (PDF 931 KB) RIGHTS AND

PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Luo, Q., Yang, X., Yu, S. _et al._ Structural basis for lipopolysaccharide extraction by ABC transporter LptB2FG.

_Nat Struct Mol Biol_ 24, 469–474 (2017). https://doi.org/10.1038/nsmb.3399 Download citation * Received: 11 January 2017 * Accepted: 14 March 2017 * Published: 10 April 2017 * Issue Date:

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