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Crystal structure of a membrane-bound O-acyltransferase

Naturevolume 562pages286290 (2018) | Download Citation

Abstract

Membrane-bound O-acyltransferases (MBOATs) are a superfamily of integral transmembrane enzymes that are found in all kingdoms of life1. In bacteria, MBOATs modify protective cell-surface polymers. In vertebrates, some MBOAT enzymes—such as acyl-coenzyme A:cholesterol acyltransferase and diacylglycerol acyltransferase 1—are responsible for lipid biosynthesis or phospholipid remodelling2,3. Other MBOATs, including porcupine, hedgehog acyltransferase and ghrelin acyltransferase, catalyse essential lipid modifications of secreted proteins such as Wnt, hedgehog and ghrelin, respectively4,5,6,7,8,9,10. Although many MBOAT proteins are important drug targets, little is known about their molecular architecture and functional mechanisms. Here we present crystal structures of DltB, an MBOAT responsible for the d-alanylation of cell-wall teichoic acid in Gram-positive bacteria11,12,13,14,15,16, both alone and in complex with the d-alanyl donor protein DltC. DltB contains a ring of 11 peripheral transmembrane helices, which shield a highly conserved extracellular structural funnel extending into the middle of the lipid bilayer. The conserved catalytic histidine residue is located at the bottom of this funnel and is connected to the intracellular DltC through a narrow tunnel. Mutation of either the catalytic histidine or the DltC-binding site of DltB abolishes the d-alanylation of lipoteichoic acid and sensitizes the Gram-positive bacterium Bacillus subtilis to cell-wall stress, which suggests cross-membrane catalysis involving the tunnel. Structure-guided sequence comparison among DltB and vertebrate MBOATs reveals a conserved structural core and suggests that MBOATs from different organisms have similar catalytic mechanisms. Our structures provide a template for understanding structure–function relationships in MBOATs and for developing therapeutic MBOAT inhibitors.

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Data availability

Atomic structures have been deposited in the Protein Data Bank (PDB) with accession codes 6BUG (crystal form I), 6BUH (crystal form II) and 6BUI (crystal form III). All other data that support the findings of this study are available from the corresponding author upon reasonable request.

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Acknowledgements

We are grateful to the staff at Advanced Light Source beamlines 5.0.1, 8.2.1 and 8.2.2 for assistance with synchrotron data collection. We thank N. Zheng and P. Hsu for comments on this manuscript, T. Hinds for discussion and advice on assays, S. Ovchinnikov for computational modelling, L. Kruse for use of the radioactive gel scanner and M. Ragheb for construction of the dlt operon deletion strain. This work was supported by National Institutes of Health grant R01 GM127316 to W.X. and a Jane Coffin Childs postdoctoral fellowship to D.M. This work was also supported by Chinese Academy of Sciences grant XDB08010303 to Z.R. and W.X., the National Institute of Health grant DP2GM110773 to H.M. and the Bacterial Pathogenesis Training Grant 5T32AI055396-13 to K.S.L.

Reviewer information

Nature thanks E. Tate and the other anonymous reviewer(s) for their contribution to the peer review of this work.

Author information

Affiliations

  1. Department of Biological Structure, University of Washington, Seattle, WA, USA

    • Dan Ma
    • , Zhizhi Wang
    • , Xin Li
    •  & Wenqing Xu
  2. Department of Microbiology, University of Washington, Seattle, WA, USA

    • Christopher N. Merrikh
    • , Kevin S. Lang
    •  & Houra Merrikh
  3. Department of Biochemistry, University of Washington, Seattle, WA, USA

    • Peilong Lu
  4. College of Life Sciences, State Key Laboratory of Medicinal Chemistry Laboratory, Nankai University, Tianjin, China

    • Xin Li
    •  & Zihe Rao
  5. Department of Genome Sciences, University of Washington, Seattle, WA, USA

    • Houra Merrikh
  6. National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China

    • Zihe Rao
    •  & Wenqing Xu
  7. Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai, China

    • Zihe Rao
  8. University of Chinese Academy of Sciences, Beijing, China

    • Zihe Rao
  9. Laboratory of Structural Biology, School of Medicine, Tsinghua University, Beijing, China

    • Zihe Rao

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Contributions

D.M. carried out protein purification, crystallization, and related binding and enzymatic analysis. D.M. and Z.W. collected diffraction data and determined the crystal structure. Z.W. performed structural refinement. C.N.M. constructed the B. subtilis strains, and C.N.M., K.S.L. and H.M. performed the cell survival assays. P.L. contributed to molecular cloning and sample preparation. X.L. and Z.R. contributed to screening of other MBOAT proteins. D.M., Z.W. and W.X. analysed structural data and wrote the paper. All authors participated in manuscript revision and analysis of biochemical data.

Competing interests

The authors declare no competing interests.

Corresponding author

Correspondence to Wenqing Xu.

Extended data figures and tables

  1. Extended Data Fig. 1 MBOAT-catalysed reactions and chemical structures of MBOAT substrates.

    a, General reaction catalysed by MBOATs. b, Structure of CoA and acyl-CoA. The red rectangle highlights the Ppant prosthetic group within the CoA structure. For known acyl-group donors of MBOATs, the acyl groups are covalently linked with a sulfhydryl group (for example, that of Ppant in acyl-CoA or DltC-Ppant). c, Comparison of acyl-group donors and acceptors of PORCN, GOAT, DGAT1, ACAT and DltB. In the acyl-group donor column, the red dashed lines indicate the bonds that are broken during acyl-transfer reactions. In the acyl-group acceptor column, the hydroxyl groups that accept acyl groups are highlighted in red. ACAT1, ACAT2 and DGAT1 use saturated and unsaturated long-chain acyl-CoA. d, The reaction catalysed by DltB. DltB catalyses d-alanylation of both wall teichoic acid and LTA. Because the d-alanylation of wall teichoic acid is at least partially dependent on LTA d-alanylation, here we discuss only the d-alanylation of LTA. DltB transfers d-alanyl groups onto hydroxyl groups of the polyglycerolphosphate chain of the LTA molecule. For simplicity, only the type I LTA structure is shown here. The fatty-acid chains are responsible for the anchoring of LTA to the membrane of Gram-positive bacteria.

  2. Extended Data Fig. 2 Purification of DltB, DltC-Ppant and DltB mutants.

    a, SEC profile of DltB. DltB can be purified to homogeneity in most detergents and is well-behaved during SEC. b, SDS–PAGE and SEC profile of DltC. c, Mass spectrometry analysis of DltC species. This indicates that purified DltC has a molecular mass of 9,590 Da, which is equal to the calculated molecular mass of Ppant-modified DltC, referred to as DltC-Ppant. d, SEC profile of wild-type and mutant DltB proteins. DltB mutants including V305D/I306D, S293A, H289A and H336A are properly folded, as they migrate predominantly as a monomeric peak, similar to wild-type DltB.

  3. Extended Data Fig. 3 Electron density map of DltB.

    a, Stereo experimental electron density map, using phases derived from an Au-SAD phasing (Extended Data Table 1). This 2FoFc map is contoured at 1.0σ. DltB backbone tracing is shown in red. b, The final 2FoFc electron density map of the crystal form II (Extended Data Table 1). This map is contoured at 1.0σ, shown in stereo and in an orientation approximately looking down the funnel. The catalytic His336 as well as His289 (another conserved residue (either His or Asn) among MBOAT proteins) are labelled. Both His336 and His289 are located at the bottom of the extracellular funnel, and sandwich the top opening of the transmembrane tunnel.

  4. Extended Data Fig. 4 Stereo view of DltB structure, and an extracellular ‘ring’ of DltB residues associated with a switch of pathogen host.

    a, The ‘front’ side view of DltB (stereo view is provided). b, The ‘top’ view of DltB, looking from the extracellular space (stereo view is provided). The His336 side chain is shown as sticks. The extracellular funnel is clear at this angle. c, Cartoon illustration of the N- and C-ridges of DltB in two orthogonal views. d, Locations of pathogen-host-sensitive sites in S. aureus DltB (I2, V61, T113, H121, I227, Q231, Y247, Y250, Y346, G401 and K402) are labelled with red balls in corresponding residues of the S. thermophilus DltB structure. It is clear that all 11 sites are located at the apex of the extracellular ridge of DltB. S. aureus DltB T113 is not conserved and does not have a corresponding residue in other DltBs (see Extended Data Fig. 5): here, the position of its closest residue is labelled. The intracellular DltC is shown in magenta. The DltB structure in these two panels are related with a 45° rotation.

  5. Extended Data Fig. 5 DltB sequence alignment.

    DltB sequences of representatives from 10 different genera of Gram-positive bacteria were chosen for sequence alignment using the T-Coffee server. Secondary structural elements of DltB are indicated above the alignment. Residues that form the funnel are identified by purple squares, and residues that form the tunnel are identified with dark red dots. DltB residues involved in direct interaction with DltC are indicated with orange inverted triangles. Residues corresponding to the three sites for which single-point mutations desensitize S. aureus to inhibition by m-AMSA are indicated with blue triangles. Residues of S. aureus DltB, the mutation of which alter the host preference from being human-specific to being capable of infecting rabbits, are indicated with green diamonds. A red star highlights the histidine residue that is completely conserved among MBOATs. ST, S. thermophilus; BS, B. subtilis; LC, L. casei; SA, S. aureus; Lm, Listeria monocytogenes; EF, Enterococcus faecalis; CD, Clostridioides difficile; LM, Leuconostoc mesenteroides; LS, Lysinibacillus sphaericus; BT, Brochothrix thermosphacta.

  6. Extended Data Fig. 6 GST pull-down and Octet assays for analysis of the interaction between DltB and DltC-Ppant.

    a, Results of using wild-type GST–DltC to pull-down either wild-type or mutant DltB, with GST to pull-down wild-type DltB as a negative control. Lanes 1–5 show inputs in this experiment. Pull-down results demonstrate that DltB and DltC can form a stable complex at an almost 1:1 molar ratio. DltB(V305D) loses most of its capacity to bind to wild-type GST–DltC, whereas the binding between DltB and DltC was completely abolished with the double mutant DltB(V305D/I306D). b, Results of using wild-type or mutant GST–DltC to pull-down wild-type DltB. Lanes 1–5 show inputs in this experiment. The mutant GST–DltC(V39D) runs slightly slower than wild-type GST–DltC and GST–DltC(V39R) on SDS–PAGE. Both GST–DltC(V39D) and GST–DltC(V39R) lost most of their capacity to bind with wild-type DltB. Pull-down experiments were performed at least twice technically, with the same results. c. Binding-affinity measurements for DltB and DltC using the Octet technique. Wild-type GST–DltC-Ppant and GST–DltC(S35A) show similar binding affinities with wild-type DltB. Data are shown in blue, with the corresponding fits in red. The DltB concentration gradient used here is: 0.03 µM, 0.1 µM, 0.3 µM, 1 µM, 3 µM, 10 µM. Octet assays were performed twice technically. d, Summary of Octet binding assay. Wild-type DltC and GST–DltC(S35A) show similar binding affinities to wild-type DltB. Mean Kd values and s.d. are shown for each assay. Mutation of residues on the binding surface of either DltB or DltC can reduce or abolish their binding.

  7. Extended Data Fig. 7 Structural details of the DltB–DltC interface and the DltB tunnel.

    a, Superposition of crystal structures of DltB and the DltB–DltC complex. There is no significant conformational change in DltB upon the binding of DltC-Ppant. b, Cylinder illustration of the DltB–DltC-Ppant complex, viewed from the bottom of the DltB tunnel. DltB is coloured in rainbow, with DltC in purple. c, Conservation of the DltB tunnel region. Residues involved in tunnel formation are also highly conserved among DltB proteins from different species (Extended Data Fig. 5). d, Stereo view of the DltB tunnel and residues forming this tunnel. The tunnel is formed by three helices from the C-ridge (H13, H14 and H15) and the short H12 helix. Residues involved in tunnel formation in our structures are: Lys282, Trp285, Asn286, Ser293, Phe294, Phe296, Arg297, Phe301, Met302, Tyr325, Asn328, Met329, Met332, Leu353, and His336 (which is also involved in the formation of extracellular funnel).

  8. Extended Data Fig. 8 Survival and LTA d-alanylation assays for wild-type and mutant DltB.

    a, Lysozyme susceptibility survival assay. For DltB residues used in both LTA d-alanylation and survival assays, corresponding DltB residue numbers in two species are listed. The endogenous dlt operon was deleted in the B. subtilis strain and complemented with an ectopic copy of the wild-type dlt operon without tag on DltB. Representative images of serial dilutions of cells plated on LB agar (left) and LB agar supplemented with 30 µg ml−1 of lysozyme (right). The genotype of the dltB gene is indicated above the corresponding column of serial dilutions. Dilutions of cells are indicated on the y axis. Mutation of the critical histidine (His328) and residues of DltB involved in binding with DltC(V297/F298) increase the susceptibility to lysozyme of B. subtilis. b, Per cent survival of B. bacillus variants towards lysozyme treatment. This was calculated by dividing the colony-forming units (CFUs) from lysozyme plates by the CFUs from LB-only plates. Data are mean ± s.d. of three biological replicates. The genotype of dltB is indicated at the bottom. B. subtilis strains containing untagged DltB show a similar lysozyme susceptibility pattern to those containing Flag-tagged DltB. c, LTA d-alanylation assay. In experiment 1, the assay time was 120 min after 14C-d-alanine was added, whereas for experiments 2 and 3, the assay time was 30 min. Experiments 2 and 3 are two parallel assays for LTA d-alanylation detection. AMSA represents m-AMSA, a DltB inhibitor.

  9. Extended Data Fig. 9 Comparison and rationalization of topological data.

    a, Comparison of HHAT topology data with the DltB structure. b, Comparison of GOAT topology data with the DltB structure. In both panels, secondary structures above DltB sequences are generated from our DltB crystal structure. Reported topology assignments of HHAT and GOAT were achieved using human proteins. Here we highlighted the predicted HHAT or GOAT transmembrane helices for each protein with yellow background within sequences. Residues for human HHAT and GOAT that were experimentally verified to be located on the cytoplasmic side are coloured in red, and residues which are on the lumenal side are coloured in green. Helices and/or loops that are predicted to be associated with the membrane surface or buried halfway within the membrane on the cytoplasmic side are indicated with red and magenta rectangles, respectively. It is clear that the regions corresponding to DltB H7–H14 are topologically more conserved than those forming the DltB N- and C-ridges.

  10. Extended Data Table 1 Data collection, phasing and refinement statistics

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https://doi.org/10.1038/s41586-018-0568-2

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