8ier

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Cryo-EM structure of ATP13A2 in the putative of E2 state

Structural highlights

8ier is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:Electron Microscopy, Resolution 4.87Å
Ligands:SPM
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Disease

AT132_HUMAN Autosomal recessive spastic paraplegia type 78;Kufor-Rakeb syndrome;ATP13A2-related juvenile neuronal ceroid lipofuscinosis. The disease is caused by variants affecting the gene represented in this entry. KRS has also been referred to as neuronal ceroid lipofuscinosis 12 (CLN12), due to neuronal and glial lipofuscin deposits detected in the cortex, basal nuclei and cerebellum of some patients.[1] The disease is caused by variants affecting the gene represented in this entry.

Function

AT132_HUMAN ATPase which acts as a lysosomal polyamine exporter with high affinity for spermine (PubMed:31996848). Also stimulates cellular uptake of polyamines and protects against polyamine toxicity (PubMed:31996848). Plays a role in intracellular cation homeostasis and the maintenance of neuronal integrity (PubMed:22186024). Contributes to cellular zinc homeostasis (PubMed:24603074). Confers cellular protection against Mn(2+) and Zn(2+) toxicity and mitochondrial stress (PubMed:26134396). Required for proper lysosomal and mitochondrial maintenance (PubMed:22296644, PubMed:28137957). Regulates the autophagy-lysosome pathway through the control of SYT11 expression at both transcriptional and post-translational levels (PubMed:27278822). Facilitates recruitment of deacetylase HDAC6 to lysosomes to deacetylate CTTN, leading to actin polymerization, promotion of autophagosome-lysosome fusion and completion of autophagy (PubMed:30538141). Promotes secretion of exosomes as well as secretion of SCNA via exosomes (PubMed:25392495, PubMed:24603074). Plays a role in lipid homeostasis (PubMed:31132336).[2] [3] [4] [5] [6] [7] [8] [9] [10] [11]

Publication Abstract from PubMed

Dysregulation of polyamine homeostasis strongly associates with human diseases. ATP13A2, which is mutated in juvenile-onset Parkinson's disease and autosomal recessive spastic paraplegia 78, is a transporter with a critical role in balancing the polyamine concentration between the lysosome and the cytosol. Here, to better understand human ATP13A2-mediated polyamine transport, we use single-particle cryo-electron microscopy to solve high-resolution structures of human ATP13A2 in six intermediate states, including the putative E2 structure for the P5 subfamily of the P-type ATPases. These structures comprise a nearly complete conformational cycle spanning the polyamine transport process and capture multiple substrate binding sites distributed along the transmembrane regions, suggesting a potential polyamine transport pathway. Integration of high-resolution structures, biochemical assays, and molecular dynamics simulations allows us to obtain a better understanding of the structural basis of how hATP13A2 transports polyamines, providing a mechanistic framework for ATP13A2-related diseases.

Conformational cycle of human polyamine transporter ATP13A2.,Mu J, Xue C, Fu L, Yu Z, Nie M, Wu M, Chen X, Liu K, Bu R, Huang Y, Yang B, Han J, Jiang Q, Chan KC, Zhou R, Li H, Huang A, Wang Y, Liu Z Nat Commun. 2023 Apr 8;14(1):1978. doi: 10.1038/s41467-023-37741-0. PMID:37031211[12]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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Citations
1 reviews cite this structure
P-type ATPases: Many more enigmas left to solve.
Palmgren et al. (2023)
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References

  1. ↑ Bras J, Verloes A, Schneider SA, Mole SE, Guerreiro RJ. Mutation of the parkinsonism gene ATP13A2 causes neuronal ceroid-lipofuscinosis. Hum Mol Genet. 2012 Jun 15;21(12):2646-50. doi: 10.1093/hmg/dds089. Epub 2012 Mar, 2. PMID:22388936 doi:http://dx.doi.org/10.1093/hmg/dds089
  2. ↑ Ramonet D, Podhajska A, Stafa K, Sonnay S, Trancikova A, Tsika E, Pletnikova O, Troncoso JC, Glauser L, Moore DJ. PARK9-associated ATP13A2 localizes to intracellular acidic vesicles and regulates cation homeostasis and neuronal integrity. Hum Mol Genet. 2012 Apr 15;21(8):1725-43. doi: 10.1093/hmg/ddr606. Epub 2011 Dec , 20. PMID:22186024 doi:http://dx.doi.org/10.1093/hmg/ddr606
  3. ↑ Grunewald A, Arns B, Seibler P, Rakovic A, Munchau A, Ramirez A, Sue CM, Klein C. ATP13A2 mutations impair mitochondrial function in fibroblasts from patients with Kufor-Rakeb syndrome. Neurobiol Aging. 2012 Aug;33(8):1843.e1-7. doi:, 10.1016/j.neurobiolaging.2011.12.035. Epub 2012 Jan 31. PMID:22296644 doi:http://dx.doi.org/10.1016/j.neurobiolaging.2011.12.035
  4. ↑ Kong SM, Chan BK, Park JS, Hill KJ, Aitken JB, Cottle L, Farghaian H, Cole AR, Lay PA, Sue CM, Cooper AA. Parkinson's disease-linked human PARK9/ATP13A2 maintains zinc homeostasis and promotes alpha-Synuclein externalization via exosomes. Hum Mol Genet. 2014 Jun 1;23(11):2816-33. doi: 10.1093/hmg/ddu099. Epub 2014 Mar , 6. PMID:24603074 doi:http://dx.doi.org/10.1093/hmg/ddu099
  5. ↑ Tsunemi T, Hamada K, Krainc D. ATP13A2/PARK9 regulates secretion of exosomes and alpha-synuclein. J Neurosci. 2014 Nov 12;34(46):15281-7. doi: 10.1523/JNEUROSCI.1629-14.2014. PMID:25392495 doi:http://dx.doi.org/10.1523/JNEUROSCI.1629-14.2014
  6. ↑ Holemans T, Sorensen DM, van Veen S, Martin S, Hermans D, Kemmer GC, Van den Haute C, Baekelandt V, Gunther Pomorski T, Agostinis P, Wuytack F, Palmgren M, Eggermont J, Vangheluwe P. A lipid switch unlocks Parkinson's disease-associated ATP13A2. Proc Natl Acad Sci U S A. 2015 Jul 21;112(29):9040-5. doi:, 10.1073/pnas.1508220112. Epub 2015 Jul 1. PMID:26134396 doi:http://dx.doi.org/10.1073/pnas.1508220112
  7. ↑ Bento CF, Ashkenazi A, Jimenez-Sanchez M, Rubinsztein DC. The Parkinson's disease-associated genes ATP13A2 and SYT11 regulate autophagy via a common pathway. Nat Commun. 2016 Jun 9;7:11803. doi: 10.1038/ncomms11803. PMID:27278822 doi:http://dx.doi.org/10.1038/ncomms11803
  8. ↑ Estrada-Cuzcano A, Martin S, Chamova T, Synofzik M, Timmann D, Holemans T, Andreeva A, Reichbauer J, De Rycke R, Chang DI, van Veen S, Samuel J, Schols L, Poppel T, Mollerup Sorensen D, Asselbergh B, Klein C, Zuchner S, Jordanova A, Vangheluwe P, Tournev I, Schule R. Loss-of-function mutations in the ATP13A2/PARK9 gene cause complicated hereditary spastic paraplegia (SPG78). Brain. 2017 Feb;140(2):287-305. doi: 10.1093/brain/aww307. PMID:28137957 doi:http://dx.doi.org/10.1093/brain/aww307
  9. ↑ Wang R, Tan J, Chen T, Han H, Tian R, Tan Y, Wu Y, Cui J, Chen F, Li J, Lv L, Guan X, Shang S, Lu J, Zhang Z. ATP13A2 facilitates HDAC6 recruitment to lysosome to promote autophagosome-lysosome fusion. J Cell Biol. 2019 Jan 7;218(1):267-284. doi: 10.1083/jcb.201804165. Epub 2018 Dec, 11. PMID:30538141 doi:http://dx.doi.org/10.1083/jcb.201804165
  10. ↑ Marcos AL, Corradi GR, Mazzitelli LR, Casali CI, Fernandez Tome MDC, Adamo HP, de Tezanos Pinto F. The Parkinson-associated human P5B-ATPase ATP13A2 modifies lipid homeostasis. Biochim Biophys Acta Biomembr. 2019 Oct 1;1861(10):182993. doi:, 10.1016/j.bbamem.2019.05.015. Epub 2019 May 24. PMID:31132336 doi:http://dx.doi.org/10.1016/j.bbamem.2019.05.015
  11. ↑ van Veen S, Martin S, Van den Haute C, Benoy V, Lyons J, Vanhoutte R, Kahler JP, Decuypere JP, Gelders G, Lambie E, Zielich J, Swinnen JV, Annaert W, Agostinis P, Ghesquiere B, Verhelst S, Baekelandt V, Eggermont J, Vangheluwe P. ATP13A2 deficiency disrupts lysosomal polyamine export. Nature. 2020 Feb;578(7795):419-424. doi: 10.1038/s41586-020-1968-7. Epub 2020 Jan, 29. PMID:31996848 doi:http://dx.doi.org/10.1038/s41586-020-1968-7
  12. ↑ Mu J, Xue C, Fu L, Yu Z, Nie M, Wu M, Chen X, Liu K, Bu R, Huang Y, Yang B, Han J, Jiang Q, Chan KC, Zhou R, Li H, Huang A, Wang Y, Liu Z. Conformational cycle of human polyamine transporter ATP13A2. Nat Commun. 2023 Apr 8;14(1):1978. PMID:37031211 doi:10.1038/s41467-023-37741-0

Contents


PDB ID 8ier

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