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Structure of human glycosylphosphatidylinositol transamidase

Nature Structural & Molecular Biology volume 29, pages 203–209 (2022)Cite this article

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Abstract

Glycosylphosphatidylinositol (GPI) molecules are complex glycophospholipids and serve as membrane anchors for tethering many proteins to the cell surface. Attaching GPI to the protein in the endoplasmic reticulum (ER) is catalyzed by the transmembrane GPI transamidase (GPIT) complex, which is essential for maturation of the GPI-anchored proteins. The GPIT complex is known to be composed of five subunits: PIGK, PIGU, PIGT, PIGS and GPAA1. Here, we determined the structure of the human GPIT complex at a resolution of 3.1 Å using single-particle cryo-EM, elucidating its overall assembly. The PIGK subunit functions as the catalytic component, in which we identified a C206-H164-N58 triad that is critical for the transamination reaction. Transmembrane helices constitute a widely opened cleft, which is located underneath PIGK, serving as a GPI substrate-binding site. The ubiquitin E3 ligase RNF121 is visualized at the back of the complex and probably serves as a quality control factor for the GPIT complex.

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Fig. 1: Architecture of human GPIT complex.
Fig. 2: Interactions between subunits.
Fig. 3: Structural and functional characterization of the PIGK subunit.
Fig. 4: GPI-binding site of the GPIT complex.

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Data availability

The three-dimensional cryo-EM density maps of the GPIT and GPIT-RNF121 complexes have been deposited in the EM Database under accession codes EMD-32336 and EMD-32452, respectively, and the coordinates of the GPIT complex have been deposited in the Protein Data Bank under accession code 7W72. Source data are provided with this paper.

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Acknowledgements

We thank B. Zhu, J. Xiong, Z. Liu and S. Zhou from the Institute of Biophysics, Chinese Academy of Science, for helpful discussion about the PIGK knockout experiment. We thank M. Dong from the National Institute of Biological Science, Beijing, and M. Zhou from Nanjing University of Science and Technology, China, for helpful discussion about the mass spectrometry experiment. We thank X. Huang, B. Zhu, X. Li and other staff members at the Center for Biological Imaging (CBI), Core Facilities for Protein Science at the Institute of Biophysics, Chinese Academy of Science (IBP, CAS) for support in cryo-EM data collection. We thank J. Jia and S. Meng (Core Facility of Institute of Biophysics, Chinese Academy of Sciences) for flow cytometric analysis. We thank X. Ding and M. Zhang from the Laboratory of Proteomics, Core Facility of Protein Science, Institute of Biophysics, Chinese Academy of Sciences, for mass spectrometry analysis. We thank Y. Wu for his research assistant service. This work is funded by National Natural Science Foundation of China (grants 92157102, to Y.Z., and 31971134, to X.C.Z.), National Key Research and Development Program of China (grant 2021YFA1301501, to Y.Z.) and Chinese Academy of Sciences Strategic Priority Research Program (grants XDB37030304, to Y.Z., and XDB08020301 and XDB37030301, to X.C.Z.).

Author information

Author notes

  1. These authors contributed equally: Hongwei Zhang, Jiawei Su, Bin Li.

Authors and Affiliations

  1. National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China

    Hongwei Zhang, Jiawei Su, Bin Li, Yiwei Gao, Mengran Liu, Lingli He, Hao Xu, Yanli Dong, Xuejun Cai Zhang & Yan Zhao

  2. College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China

    Hongwei Zhang, Jiawei Su, Bin Li, Yiwei Gao, Mengran Liu, Lingli He, Xuejun Cai Zhang & Yan Zhao

  3. Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China

    Hao Xu

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Contributions

Y.Z. conceived and supervised the project. H.Z. and M.L. carried out molecular cloning. H.Z. expressed purified protein complex samples and prepared samples for cryo-EM study. H.Z. and Y.G. carried out cryo-EM data collection. B.L., Y.G., H.X. and Y.Z. processed the cryo-EM data, built models and prepared figures. J.S. and L.H. made the PIGK-deficient HEK293 cell line. H.Z., J.S., L.H. and Y.D. carried out confocal microscopy and flow cytometric analyses. X.C.Z. and Y.Z. analyzed the structure and wrote the manuscript with input from all authors.

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Correspondence to Yan Zhao.

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Nature Structural and Molecular Biology thanks Calvin Yip and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Peer reviewer reports are available. Florian Ullrich was the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

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Extended data

Extended Data Fig. 1 Purification of the human GPIT complex.

a, Size−exclusive chromatography (Superose 6 increase) of purified sample of human GPIT complex. Peak fractions within the dashed lines were collected for cryo-EM sample preparation. b, Coomassie−blue-stained SDS-PAGE gel of SEC peak fractions. GPIT components are labeled. The bands of PIGS and PIGK are smeared because of varied extent of glycosylation. The experiments were repeated independently more than 3 times with similar results.

Source data

Extended Data Fig. 2 Cryo-EM analysis of the GPITX complex.

a, Flow chart of cryo-EM data processing of the human GPITX complex. A total of 2,795 movie stacks were collected. A representative motion-corrected micrograph of this dataset is shown here. Particles were picked using Topaz and Gautomatch, and were then submitted to 2D and 3D classifications, followed by Bayesian polish, and CTF refinement and 3D-auto refinement. The final map of GPITX and GPIT was reported at 3.8 Å and 3.4 Å according to GSFSC criterion, respectively. b, Sharpened map of human GPITX complex, colored according to the estimation of local resolution. c, Angular distribution of particles contributed to the final reconstruction. The length of cylinders indicates the number of particles in the designated orientation. d, Half-map FSC curves of human GPIT complex, calculated before (red) and after (blue) PostProcesss.

Extended Data Fig. 3 Cryo-EM data processing of the human GPIT complex.

a, Flow chart of cryo-EM data processing of the human GPIT complex. A total of 2,186 movie stacks were collected (Bar = 40 nm). A representative motion-corrected micrograph of this dataset is shown here. Particles were picked using Gautomatch, Topaz, and Template Picker in cryoSPARC, and were then submitted to several rounds of 3D classification, Bayesian polish, and CTF and 3D-auto refinement. The final map was reported at 3.1 Å according to GSFSC criterion. b, Sharpened map of human GPIT complex, colored according to the estimation of local resolution. c, Angular distribution of particles contributed to the final reconstruction. The length of cylinders indicates the number of particles in the designated orientation. d, Half-map and model-map FSC curves of human GPIT complex. Half-map FSC curves were calculated before (red) and after (blue) PostProcesss, overlaid with a model-map FSC which is calculated between the final map and structural model. e, Representative EM maps for the human GPIT complex and the GPI molecule.

Extended Data Fig. 4 Structural comparison of PIGU and GPAA1 with homologous structures.

a, Side view and top-down view of the subunit PIGU, colored in a rainbow scheme. b, Structural comparison between PIGU and ALG6. The substrate of ALG6 (Dol25-P-Glc) is shown as sticks. c, Structural comparison between GPAA1 and AMPX. Critical residues and hydroxamate are shown as sticks. The zinc ions are shown as spheres.

Extended Data Fig. 5 Distribution of the pathogenic mutations in the GPIT complex.

a-b, Side-view of the structures of the GPIT complex. The Cα atoms of the pathogenic mutations are shown in spheres. c, Reported pathogenic mutations and related diseases are listed.

Extended Data Fig. 6 More analyses on the catalytic site in PIGK.

a, Sequence alignment of human legumain and PIGK. Secondary structures are marked above the alignment. Red triangles indicate residues that are critical for the endopeptidase activity. b, Florescent confocal microscopy analyses of effects of N58KA and D120KN on GPIT activity using HEK293ΔPIGK cells as the host. The first, second, and third columns represent the confocal fluorescence microscopy of GFP, mCherry, and merged images, respectively. The scale bar represents 10 μm. The confocal microscopy experiment was repeated at least five times.

Source data

Extended Data Fig. 7 GPIT activity detected in flow cytometry experiment.

a, Cartoon scheme of GPIT activity analysis using GSTCy5-nanobodyGFP. b, The gating strategy for FACS. HEK293T cells was first gated on FSC and SSC signals (R1). GFP and Cy5 positive cells were defined as cells exceeding fluorescence of wild type cells (R2). c, The HEK293 cells (WT or PIGK deficient) expressing GFP-GPI and PIGK (WT or mutants) are analyzed according to GFP and Cy5 fluorescence using flow cytometry. Cells was first gated on FSC and SSC signals. GFP and Cy5 positive cells were defined as cells exceeding fluorescence of wild type cells. The flow cytometry experiment was repeated at least five times.

Extended Data Fig. 8 Sequence alignment of the GPI binding site.

Analysis of amino acid sequences of PIGU and PIGT homologous. HsPIGU and HsPIGT is from Homo sapiens (Uniprot ID: Q9H490 and Q969N2); MmPIGU-MmPIGT, Mus musculus (Q8K358 and Q8BXQ2); DrPIGU-DrPIGT, Danio rerio (F1RES7 and E9QH65); BdPIGU-BdPIGT, Bactrocera dorsalis (A0A6I9VB87 and A0A034WF00); CePIGU-CePIGT, Caenorhabditis elegans (Q22672 and Q19518); ScPIGU-ScPIGT, Saccharomyces cerevisiae (P41733 and P38875); AtPIGU-AtPIGT, Arabidopsis thaliana (F4I1Z0 and Q949U5); AfPIGU-AfPIGT, Aspergillus fumigatus (A0A0J5PDP8 and Q4WMR2); DdPIGU-DdPIGT, Dictyostelium discoideum (Q54T45 and B0G182). Secondary structures are marked above the alignment. Red triangles indicate residues that are involved in binding of the GPI molecule.

Extended Data Fig. 9 Analysis of the extra subunit of GPIT complex.

a, Cryo-EM map of the GPIT complex with six additional transmembrane helices, viewed in parallel to the membrane plane. Subunits PIGK, GPAA1, PIGU, PIGS, and PIGT are colored in cyan, blue, purple, pink, and red, respectively. The extra helices are colored in grey. b, Mass-spectrometry analysis of the purified GPIT protein sample. Subunits of GPIT complexes are highlighted in green. The putative extra subunit RNF121 is highlighted in red. c, Manually-built poly-alanine model of the extra subunit, overlaid with corresponding cryo-EM map (left). 3D structure of the RNF121 predicted by AlphaFold2 (middle); superimposition of structures of extra subunit and RNF121 (right). d, Top-down view of the transmembrane domain of the GPIT-RNF121 complex. e, Western blot analysis of strep tag purified samples (co-expressed GPIT-RNF121 or RNF121 alone) using antibodies against His tag and strep tag to monitor RNF121 and PIGU, respectively. The letters S and E represent supernatant of detergent solubilized cell membrane and elution sample from streptavidin beads, respectively. The experiments were repeated independently 3 times with similar results.

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Unprocessed microscopy images.

Source Data Extended Data Fig. 1

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Source Data Extended Data Fig. 6

Unprocessed microscopy images.

Source Data Extended Data Fig. 9

Unprocessed western blots.

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Zhang, H., Su, J., Li, B. et al. Structure of human glycosylphosphatidylinositol transamidase. Nat Struct Mol Biol 29, 203–209 (2022). https://doi.org/10.1038/s41594-022-00726-6

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