Structural basis of the acyl-transfer mechanism of human GPAT1.


Journal

Nature structural & molecular biology
ISSN: 1545-9985
Titre abrégé: Nat Struct Mol Biol
Pays: United States
ID NLM: 101186374

Informations de publication

Date de publication:
01 2023
Historique:
received: 15 06 2022
accepted: 31 10 2022
pubmed: 16 12 2022
medline: 24 1 2023
entrez: 15 12 2022
Statut: ppublish

Résumé

Glycerol-3-phosphate acyltransferase (GPAT)1 is a mitochondrial outer membrane protein that catalyzes the first step of de novo glycerolipid biosynthesis. Hepatic expression of GPAT1 is linked to liver fat accumulation and the severity of nonalcoholic fatty liver diseases. Here we present the cryo-EM structures of human GPAT1 in substrate analog-bound and product-bound states. The structures reveal an N-terminal acyltransferase domain that harbors important catalytic motifs and a tightly associated C-terminal domain that is critical for proper protein folding. Unexpectedly, GPAT1 has no transmembrane regions as previously proposed but instead associates with the membrane via an amphipathic surface patch and an N-terminal loop-helix region that contains a mitochondrial-targeting signal. Combined structural, computational and functional studies uncover a hydrophobic pathway within GPAT1 for lipid trafficking. The results presented herein lay a framework for rational inhibitor development for GPAT1.

Identifiants

pubmed: 36522428
doi: 10.1038/s41594-022-00884-7
pii: 10.1038/s41594-022-00884-7
doi:

Substances chimiques

Glycerol-3-Phosphate O-Acyltransferase EC 2.3.1.15

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

22-30

Informations de copyright

© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.

Références

Wendel, A. A., Lewin, T. M. & Coleman, R. A. Glycerol-3-phosphate acyltransferases: rate limiting enzymes of triacylglycerol biosynthesis. Biochim. Biophys. Acta 1791, 501–506 (2009).
doi: 10.1016/j.bbalip.2008.10.010
Bell, R. M. & Coleman, R. A. Enzymes of glycerolipid synthesis in eukaryotes. Annu. Rev. Biochem. 49, 459–487 (1980).
doi: 10.1146/annurev.bi.49.070180.002331
Yet, S. F., Lee, S., Hahm, Y. T. & Sul, H. S. Expression and identification of p90 as the murine mitochondrial glycerol-3-phosphate acyltransferase. Biochemistry 32, 9486–9491 (1993).
doi: 10.1021/bi00087a029
Ganesh Bhat, B. et al. Rat sn-glycerol-3-phosphate acyltransferase: molecular cloning and characterization of the cDNA and expressed protein. Biochim. Biophys. Acta 1439, 415–423 (1999).
doi: 10.1016/S1388-1981(99)00103-1
Haldar, D., Tso, W. W. & Pullman, M. E. The acylation of sn-glycerol 3-phosphate in mammalian organs and Ehrlich ascites tumor cells. J. Biol. Chem. 254, 4502–4509 (1979).
doi: 10.1016/S0021-9258(17)30039-X
Gonzalez-Baro, M. R. & Coleman, R. A. Mitochondrial acyltransferases and glycerophospholipid metabolism. Biochim. Biophys. Acta 1862, 49–55 (2017).
doi: 10.1016/j.bbalip.2016.06.023
Ross, T. T. et al. Acetyl-CoA carboxylase inhibition improves multiple dimensions of NASH pathogenesis in model systems. Cell. Mol. Gastroenterol. Hepatol. 10, 829–851 (2020).
doi: 10.1016/j.jcmgh.2020.06.001
Hakim, A. et al. Genetic variation in the mitochondrial glycerol-3-phosphate acyltransferase is associated with liver injury. Hepatology 74, 3394–3408 (2021).
doi: 10.1002/hep.32038
Liao, K. et al. Glycerol-3-phosphate acyltransferase1 is a model-agnostic node in nonalcoholic fatty liver disease: implications for drug development and precision medicine. ACS Omega 5, 18465–18471 (2020).
doi: 10.1021/acsomega.0c02350
Ellis, J. M. et al. Mice deficient in glycerol-3-phosphate acyltransferase-1 have a reduced susceptibility to liver cancer. Toxicol. Pathol. 40, 513–521 (2012).
doi: 10.1177/0192623311432298
Lewin, T. M. et al. Mice deficient in mitochondrial glycerol-3-phosphate acyltransferase-1 have diminished myocardial triacylglycerol accumulation during lipogenic diet and altered phospholipid fatty acid composition. Biochim. Biophys. Acta 1781, 352–358 (2008).
doi: 10.1016/j.bbalip.2008.05.001
Wendel, A. A. et al. Glycerol-3-phosphate acyltransferase 1 deficiency in ob/ob mice diminishes hepatic steatosis but does not protect against insulin resistance or obesity. Diabetes 59, 1321–1329 (2010).
doi: 10.2337/db09-1380
Turnbull, A. P. et al. Analysis of the structure, substrate specificity, and mechanism of squash glycerol-3-phosphate (1)-acyltransferase. Structure 9, 347–353 (2001).
doi: 10.1016/S0969-2126(01)00595-0
Tamada, T. et al. Substrate recognition and selectivity of plant glycerol-3-phosphate acyltransferases (GPATs) from Cucurbita moscata and Spinacea oleracea. Acta Crystallogr. D Biol. Crystallogr. 60, 13–21 (2004).
doi: 10.1107/S0907444903020778
Pellon-Maison, M., Coleman, R. A. & Gonzalez-Baro, M. R. The C-terminal region of mitochondrial glycerol-3-phosphate acyltransferase-1 interacts with the active site region and is required for activity. Arch. Biochem. Biophys. 450, 157–166 (2006).
doi: 10.1016/j.abb.2006.03.009
Karen, M. N., Stephanie, A. F. & Stephen, P. F. M. Synthesis and inhibitory activity of difluoroketone substrate analogs of N-myristoyltransferase. Tetrahedron 50, 9847–9864 (1994).
doi: 10.1016/S0040-4020(01)89601-0
Albesa-Jove, D. et al. Structural basis for selective recognition of acyl chains by the membrane-associated acyltransferase PatA. Nat. Commun. 7, 10906 (2016).
doi: 10.1038/ncomms10906
Robertson, R. M. et al. A two-helix motif positions the lysophosphatidic acid acyltransferase active site for catalysis within the membrane bilayer. Nat. Struct. Mol. Biol. 24, 666–671 (2017).
doi: 10.1038/nsmb.3436
Gonzalez-Baro, M. R., Granger, D. A. & Coleman, R. A. Mitochondrial glycerol phosphate acyltransferase contains two transmembrane domains with the active site in the N-terminal domain facing the cytosol. J. Biol. Chem. 276, 43182–43188 (2001).
doi: 10.1074/jbc.M107885200
Lewin, T. M., Wang, P. & Coleman, R. A. Analysis of amino acid motifs diagnostic for the sn-glycerol-3-phosphate acyltransferase reaction. Biochemistry 38, 5764–5771 (1999).
doi: 10.1021/bi982805d
Heath, R. J. & Rock, C. O. A conserved histidine is essential for glycerolipid acyltransferase catalysis. J. Bacteriol. 180, 1425–1430 (1998).
doi: 10.1128/JB.180.6.1425-1430.1998
Dircks, L. K., Ke, J. & Sul, H. S. A conserved seven amino acid stretch important for murine mitochondrial glycerol-3-phosphate acyltransferase activity. Significance of arginine 318 in catalysis. J. Biol. Chem. 274, 34728–34734 (1999).
doi: 10.1074/jbc.274.49.34728
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
doi: 10.1038/s41586-021-03819-2
Varadi, M. et al. AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Res. 50, D439–D444 (2022).
doi: 10.1093/nar/gkab1061
Mol, A. R., Castro, M. S. & Fontes, W. NetWheels: a web application to create high quality peptide helical wheel and net projections. Preprint at bioRxiv https://doi.org/10.1101/416347 (2018).
Pettersen, E. F. et al. UCSF Chimera—a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004).
doi: 10.1002/jcc.20084
Breitsprecher, D., Fung, P. A. & Tschammer, N. Improving biosensor assay development by determining sample quality with Tycho NT.6. Nat. Methods 15, 298 (2018).
doi: 10.1038/nmeth.f.406
Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36–51 (2005).
doi: 10.1016/j.jsb.2005.07.007
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nat. Methods 14, 331–332 (2017).
doi: 10.1038/nmeth.4193
Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).
doi: 10.1016/j.jsb.2015.08.008
Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018).
doi: 10.7554/eLife.42166
Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017).
doi: 10.1038/nmeth.4169
Bepler, T. et al. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nat. Methods 16, 1153–1160 (2019).
doi: 10.1038/s41592-019-0575-8
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).
doi: 10.1107/S0907444904019158
Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr. 67, 235–242 (2011).
doi: 10.1107/S0907444910045749
Stein, P. E. et al. The crystal structure of pertussis toxin. Structure 2, 45–57 (1994).
doi: 10.1016/S0969-2126(00)00007-1
Ten Eyck, L. F. Efficient structure–factor calculation for large molecules by the fast Fourier transform. Acta Crystallogr. A 33, 486–492 (1977).
doi: 10.1107/S0567739477001211
Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).
doi: 10.1107/S0907444909052925
Brown, A. et al. Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions. Acta Crystallogr. D Biol. Crystallogr. 71, 136–153 (2015).
doi: 10.1107/S1399004714021683
Nicholls, R. A., Fischer, M., McNicholas, S. & Murshudov, G. N. Conformation-independent structural comparison of macromolecules with ProSMART. Acta Crystallogr. D Biol. Crystallogr. 70, 2487–2499 (2014).
doi: 10.1107/S1399004714016241
Chen, V. B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr. 66, 12–21 (2010).
doi: 10.1107/S0907444909042073
Schrödinger, L. & DeLano, W. PyMOL http://www.pymol.org/pymol (2020).
Doerr, S., Harvey, M. J., Noe, F. & De Fabritiis, G. HTMD: high-throughput molecular dynamics for molecular discovery. J. Chem. Theory Comput. 12, 1845–1852 (2016).
doi: 10.1021/acs.jctc.6b00049
Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 27–38 (1996).
doi: 10.1016/0263-7855(96)00018-5
Harvey, M. J., Giupponi, G. & Fabritiis, G. D. ACEMD: accelerating biomolecular dynamics in the microsecond time scale. J. Chem. Theory Comput. 5, 1632–1639 (2009).
doi: 10.1021/ct9000685
Huang, J. & MacKerell, A. D. Jr. CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. J. Comput. Chem. 34, 2135–2145 (2013).
doi: 10.1002/jcc.23354
Vassetti, D., Pagliai, M. & Procacci, P. Assessment of GAFF2 and OPLS-AA general force fields in combination with the water models TIP3P, SPCE, and OPC3 for the solvation free energy of druglike organic molecules. J. Chem. Theory Comput. 15, 1983–1995 (2019).
doi: 10.1021/acs.jctc.8b01039
Scherer, M. K. et al. PyEMMA 2: a software package for estimation, validation, and analysis of Markov models. J. Chem. Theory Comput. 11, 5525–5542 (2015).
doi: 10.1021/acs.jctc.5b00743
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
doi: 10.1038/nmeth.2019
Bolte, S. & Cordelieres, F. P. A guided tour into subcellular colocalization analysis in light microscopy. J. Microsc. 224, 213–232 (2006).
doi: 10.1111/j.1365-2818.2006.01706.x

Auteurs

Zachary Lee Johnson (ZL)

Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA.

Mark Ammirati (M)

Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA.

David Jonathan Wasilko (DJ)

Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA.

Jeanne S Chang (JS)

Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA.

Stephen Noell (S)

Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA.

Timothy L Foley (TL)

Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA.

Hyejin Yoon (H)

Internal Medicine Research Unit, Pfizer Inc., Cambridge, MA, USA.

Kathleen Smith (K)

Internal Medicine Research Unit, Pfizer Inc., Cambridge, MA, USA.

Shoh Asano (S)

Internal Medicine Research Unit, Pfizer Inc., Cambridge, MA, USA.

Katherine Hales (K)

Internal Medicine Research Unit, Pfizer Inc., Cambridge, MA, USA.

Min Wan (M)

Internal Medicine Research Unit, Pfizer Inc., Cambridge, MA, USA.

Qingyi Yang (Q)

Internal Medicine, Medicine Design, Pfizer Inc., Cambridge, MA, USA.

Mary A Piotrowski (MA)

Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA.

Kathleen A Farley (KA)

Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA.

Tamara Gilbert (T)

Internal Medicine Research Unit, Pfizer Inc., Cambridge, MA, USA.

Lisa M Aschenbrenner (LM)

Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA.

Kimberly F Fennell (KF)

Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA.

Jason K Dutra (JK)

Internal Medicine, Medicine Design, Pfizer Inc., Groton, CT, USA.

Mary Xu (M)

Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA.

Chunyang Guo (C)

Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA.

Alison E Varghese (AE)

Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA.

Justin Bellenger (J)

Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA.

Alandra Quinn (A)

Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA.

Christopher W Am Ende (CW)

Internal Medicine, Medicine Design, Pfizer Inc., Groton, CT, USA.

Graham M West (GM)

Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA.

Matthew C Griffor (MC)

Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA.

Donald Bennett (D)

Biostatistics, Early Clinical Development, Pfizer Inc., Cambridge, MA, USA.

Matthew Calabrese (M)

Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA.

Claire M Steppan (CM)

Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA.

Seungil Han (S)

Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA.

Huixian Wu (H)

Discovery Sciences, Medicine Design, Pfizer Inc., Groton, CT, USA. huixian.wu@pfizer.com.

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