Structure of the AAA Protein Msp1 Reveals Mechanism of Mislocalized Membrane Protein Extraction

Overview

Journal Elife

Specialty Biology

Date 2020 Jan 31

PMID 31999255

Citations 26

Authors

Lan Wang

Alexander Myasnikov

Xingjie Pan

Peter Walter

Affiliations

Soon will be listed here.

Abstract

The AAA protein Msp1 extracts mislocalized tail-anchored membrane proteins and targets them for degradation, thus maintaining proper cell organization. How Msp1 selects its substrates and firmly engages them during the energetically unfavorable extraction process remains a mystery. To address this question, we solved cryo-EM structures of Msp1-substrate complexes at near-atomic resolution. Akin to other AAA proteins, Msp1 forms hexameric spirals that translocate substrates through a central pore. A singular hydrophobic substrate recruitment site is exposed at the spiral's seam, which we propose positions the substrate for entry into the pore. There, a tight web of aromatic amino acids grips the substrate in a sequence-promiscuous, hydrophobic milieu. Elements at the intersubunit interfaces coordinate ATP hydrolysis with the subunits' positions in the spiral. We present a comprehensive model of Msp1's mechanism, which follows general architectural principles established for other AAA proteins yet specializes Msp1 for its unique role in membrane protein extraction.

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References

Augustin S, Gerdes F, Lee S, Tsai F, Langer T, Tatsuta T . An intersubunit signaling network coordinates ATP hydrolysis by m-AAA proteases. Mol Cell. 2009; 35(5):574-85. PMC: 2744646. DOI: 10.1016/j.molcel.2009.07.018. View

Wendler P, Ciniawsky S, Kock M, Kube S . Structure and function of the AAA+ nucleotide binding pocket. Biochim Biophys Acta. 2011; 1823(1):2-14. DOI: 10.1016/j.bbamcr.2011.06.014. View

Monroe N, Han H, Shen P, Sundquist W, Hill C . Structural basis of protein translocation by the Vps4-Vta1 AAA ATPase. Elife. 2017; 6. PMC: 5413351. DOI: 10.7554/eLife.24487. View

Martin A, Baker T, Sauer R . Pore loops of the AAA+ ClpX machine grip substrates to drive translocation and unfolding. Nat Struct Mol Biol. 2008; 15(11):1147-51. PMC: 2610342. DOI: 10.1038/nsmb.1503. View

Yang B, Stjepanovic G, Shen Q, Martin A, Hurley J . Vps4 disassembles an ESCRT-III filament by global unfolding and processive translocation. Nat Struct Mol Biol. 2015; 22(6):492-8. PMC: 4456219. DOI: 10.1038/nsmb.3015. View

Rampello A, Glynn S . Identification of a Degradation Signal Sequence within Substrates of the Mitochondrial i-AAA Protease. J Mol Biol. 2017; 429(6):873-885. PMC: 5402353. DOI: 10.1016/j.jmb.2017.02.009. View

Umanah G, Pignatelli M, Yin X, Chen R, Crawford J, Neifert S . Thorase variants are associated with defects in glutamatergic neurotransmission that can be rescued by Perampanel. Sci Transl Med. 2017; 9(420). PMC: 6573025. DOI: 10.1126/scitranslmed.aah4985. View

Roll-Mecak A, Vale R . Structural basis of microtubule severing by the hereditary spastic paraplegia protein spastin. Nature. 2008; 451(7176):363-7. PMC: 2882799. DOI: 10.1038/nature06482. View

Scheres S . RELION: implementation of a Bayesian approach to cryo-EM structure determination. J Struct Biol. 2012; 180(3):519-30. PMC: 3690530. DOI: 10.1016/j.jsb.2012.09.006. View

10.

Zhang J, Wang Y, Chi Z, Keuss M, Pai Y, Kang H . The AAA+ ATPase Thorase regulates AMPA receptor-dependent synaptic plasticity and behavior. Cell. 2011; 145(2):284-99. PMC: 3085003. DOI: 10.1016/j.cell.2011.03.016. View

11.

Ye Y, Meyer H, Rapoport T . The AAA ATPase Cdc48/p97 and its partners transport proteins from the ER into the cytosol. Nature. 2001; 414(6864):652-6. DOI: 10.1038/414652a. View

12.

Rigden D, Liu H, Hayes S, Urbe S, Clague M . Ab initio protein modelling reveals novel human MIT domains. FEBS Lett. 2009; 583(5):872-8. DOI: 10.1016/j.febslet.2009.02.012. View

13.

Dederer V, Khmelinskii A, Huhn A, Okreglak V, Knop M, Lemberg M . Cooperation of mitochondrial and ER factors in quality control of tail-anchored proteins. Elife. 2019; 8. PMC: 6586462. DOI: 10.7554/eLife.45506. View

14.

Iyer L, Leipe D, Koonin E, Aravind L . Evolutionary history and higher order classification of AAA+ ATPases. J Struct Biol. 2004; 146(1-2):11-31. DOI: 10.1016/j.jsb.2003.10.010. View

15.

Puchades C, Ding B, Song A, Wiseman R, Lander G, Glynn S . Unique Structural Features of the Mitochondrial AAA+ Protease AFG3L2 Reveal the Molecular Basis for Activity in Health and Disease. Mol Cell. 2019; 75(5):1073-1085.e6. PMC: 6731152. DOI: 10.1016/j.molcel.2019.06.016. View

16.

Sievers F, Wilm A, Dineen D, Gibson T, Karplus K, Li W . Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011; 7:539. PMC: 3261699. DOI: 10.1038/msb.2011.75. View

17.

Bodnar N, Rapoport T . Molecular Mechanism of Substrate Processing by the Cdc48 ATPase Complex. Cell. 2017; 169(4):722-735.e9. PMC: 5751438. DOI: 10.1016/j.cell.2017.04.020. View

18.

Zehr E, Szyk A, Szczesna E, Roll-Mecak A . Katanin Grips the β-Tubulin Tail through an Electropositive Double Spiral to Sever Microtubules. Dev Cell. 2019; 52(1):118-131.e6. PMC: 7060837. DOI: 10.1016/j.devcel.2019.10.010. View

19.

Hanson P, Whiteheart S . AAA+ proteins: have engine, will work. Nat Rev Mol Cell Biol. 2005; 6(7):519-29. DOI: 10.1038/nrm1684. View

20.

Monroe N, Hill C . Meiotic Clade AAA ATPases: Protein Polymer Disassembly Machines. J Mol Biol. 2015; 428(9 Pt B):1897-911. PMC: 4860049. DOI: 10.1016/j.jmb.2015.11.004. View