Sauer, R. T. & Baker, T. A. AAA+ proteases: ATP-fueled machines of protein destruction. Annu. Rev. Biochem. 80, 587–612 (2011).
Mahmoud, S. A. & Chien, P. Regulated proteolysis in micro organism. Annu. Rev. Biochem. 87, 677–696 (2018).
Varshavsky, A. N-degron and C-degron pathways of protein degradation. Proc. Natl Acad. Sci. USA 116, 358–366 (2019).
Tobias, J. W., Shrader, T. E., Rocap, G. & Varshavsky, A. The N-end rule in micro organism. Science 254, 1374–1377 (1991).
Dougan, D. A., Reid, B. G., Horwich, A. L. & Bukau, B. ClpS, a substrate modulator of the ClpAP machine. Mol. Cell 9, 673–683 (2002).
Zeth, Okay., Dougan, D. A., Cusack, S., Bukau, B. & Ravelli, R. B. Crystallization and preliminary X-ray evaluation of the Escherichia coli adaptor protein ClpS, free and in advanced with the N-terminal area of ClpA. Acta Crystallogr. D Biol. Crystallogr. 58, 1207–1210 (2002).
Zeth, Okay. et al. Structural evaluation of the adaptor protein ClpS in advanced with the N-terminal area of ClpA. Nat. Struct. Biol. 9, 906–911 (2002).
Erbse, A. et al. ClpS is a vital part of the N-end rule pathway in Escherichia coli. Nature 439, 753–756 (2006).
Wang, Okay. H., Roman-Hernandez, G., Grant, R. A., Sauer, R. T. & Baker, T. A. The molecular foundation of N-end rule recognition. Mol. Cell 32, 406–414 (2008).
Román-Hernández, G., Grant, R. A., Sauer, R. T. & Baker, T. A. Molecular foundation of substrate choice by the N-end rule adaptor protein ClpS. Proc. Natl Acad. Sci. USA 106, 8888–8893 (2009).
Guo, F., Esser, L., Singh, S. Okay., Maurizi, M. R. & Xia, D. Crystal construction of the heterodimeric advanced of the adaptor, ClpS, with the N-domain of the AAA+ chaperone, ClpA. J. Biol. Chem. 277, 46753–46762 (2002).
De Donatis, G. M., Singh, S. Okay., Viswanathan, S. & Maurizi, M. R. A single ClpS monomer is adequate to direct the exercise of the ClpA hexamer. J. Biol. Chem. 285, 8771–8781 (2010).
Román-Hernández, G., Hou, J. Y., Grant, R. A., Sauer, R. T. & Baker, T. A. The ClpS adaptor mediates staged supply of N-end rule substrates to the AAA+ ClpAP protease. Mol. Cell 43, 217–228 (2011).
Rivera-Rivera, I., Román-Hernández, G., Sauer, R. T. & Baker, T. A. Transforming of a supply advanced permits ClpS-mediated degradation of N-degron substrates. Proc. Natl Acad. Sci. USA 111, E3853–E3859 (2014).
Torres-Delgado, A., Kotamarthi, H. C., Sauer, R. T. & Baker, T. A. The intrinsically disordered N-terminal extension of the ClpS adaptor reprograms its associate AAA+ ClpAP protease. J. Mol. Biol. 432, 4908–4921 (2020).
Hou, J. Y., Sauer, R. T. & Baker, T. A. Distinct structural components of the adaptor ClpS are required for regulating degradation by ClpAP. Nat. Struct. Mol. Biol. 15, 288–294 (2008).
Grimaud, R., Kessel, M., Beuron, F., Steven, A. C. & Maurizi, M. R. Enzymatic and structural similarities between the Escherichia coli ATP-dependent proteases, ClpXP and ClpAP. J. Biol. Chem. 273, 12476–12481 (1998).
Erzberger, J. P. & Berger, J. M. Evolutionary relationships and structural mechanisms of AAA+ proteins. Annu. Rev. Biophys. Biomol. Struct. 35, 93–114 (2006).
Kress, W., Mutschler, H. & Weber-Ban, E. Each ATPase domains of ClpA are crucial for processing of secure protein constructions. J. Biol. Chem. 284, 31441–31452 (2009).
Kotamarthi, H. C., Sauer, R. T. & Baker, T. A. The non-dominant AAA+ ring within the ClpAP protease features as an anti-stalling motor to speed up protein unfolding and translocation. Cell Rep. 30, 2644–2654 (2020).
Zuromski, Okay. L., Sauer, R. T. & Baker, T. A. Modular and coordinated exercise of AAA+ energetic websites within the double-ring ClpA unfoldase of the ClpAP protease. Proc. Natl Acad. Sci. USA 117, 25455–25463 (2020).
Zuromski, Okay. L., Kim, S., Sauer, R. T. & Baker, T. A. Division of labor between the pore-1 loops of the D1 and D2 AAA+ rings coordinates substrate selectivity of the ClpAP protease. J. Biol. Chem. 297, 101407 (2021).
Lopez, Okay. E. et al. Conformational plasticity of the ClpAP AAA+ protease {couples} protein unfolding and proteolysis. Nat. Struct. Mol. Biol. 27, 406–416 (2020).
Deville, C. et al. Structural pathway of regulated substrate switch and threading by an Hsp100 disaggregase. Sci. Adv. 3, e1701726 (2017).
Gates, S. N. et al. Ratchet-like polypeptide translocation mechanism of the AAA+ disaggregase Hsp104. Science 357, 273–279 (2017).
Yu, H. et al. ATP hydrolysis-coupled peptide translocation mechanism of Mycobacterium tuberculosis ClpB. Proc. Natl Acad. Sci. USA 115, E9560–E9569 (2018).
White, Okay. I., Zhao, M., Choi, U. B., Pfuetzner, R. A. & Brunger, A. T. Structural ideas of SNARE advanced recognition by the AAA+ protein NSF. eLife 7, e38888 (2018).
Lo, Y.-H. H. et al. Cryo-EM construction of the important ribosome meeting AAA-ATPase Rix7. Nat. Commun. 10, 513 (2019).
Rizo, A. N. et al. Structural foundation for substrate gripping and translocation by the ClpB AAA+ disaggregase. Nat. Commun. 10, 2393 (2019).
Cooney, I. et al. Construction of the Cdc48 segregase within the act of unfolding an genuine substrate. Science 365, 502–505 (2019).
Twomey, E. C. et al. Substrate processing by the Cdc48 ATPase advanced is initiated by ubiquitin unfolding. Science 365, eaax1033 (2019).
Thompson, M. W., Singh, S. Okay. & Maurizi, M. R. Processive degradation of proteins by the ATP-dependent Clp protease from Escherichia coli. Requirement for the a number of array of energetic websites in ClpP however not ATP hydrolysis. J. Biol. Chem. 269, 18209–18215 (1994).
Hoskins, J. R., Pak, M., Maurizi, M. R. & Wickner, S. The function of the ClpA chaperone in proteolysis by ClpAP. Proc. Natl Acad. Sci. USA 95, 12135–12140 (1998).
Ishikawa, T. et al. Translocation pathway of protein substrates in ClpAP protease. Proc. Natl Acad. Sci. USA 98, 4328–4333 (2001).
Effantin, G., Ishikawa, T., De Donatis, G. M., Maurizi, M. R. & Steven, A. C. Native and world mobility within the ClpA AAA+ chaperone detected by cryo-electron microscopy: useful connotations. Construction 18, 553–562 (2010).
Miller, J. M. & Lucius, A. L. ATPγS competes with ATP for binding at Area 1 however not Area 2 throughout ClpA catalyzed polypeptide translocation. Biophys. Chem. 185, 58–69 (2014).
Schlieker, C. et al. Substrate recognition by the AAA+ chaperone ClpB. Nat. Struct. Mol. Biol. 11, 607–615 (2004).
Weibezahn, J. et al. Thermotolerance requires refolding of aggregated proteins by substrate translocation by the central pore of ClpB. Cell 119, 653–665 (2004).
Hinnerwisch, J., Fenton, W. A., Furtak, Okay. J., Farr, G. W. & Horwich, A. L. Loops within the central channel of ClpA chaperone mediate protein binding, unfolding, and translocation. Cell 121, 1029–1041 (2005).
Martin, A., Baker, T. A. & Sauer, R. T. Pore loops of the AAA+ ClpX machine grip substrates to drive translocation and unfolding. Nat. Struct. Mol. Biol. 15, 1147–1151 (2008).
Doyle, S. M., Hoskins, J. R. & Wickner, S. DnaK chaperone-dependent disaggregation by caseinolytic peptidase B (ClpB) mutants reveals useful overlap within the N-terminal area and nucleotide-binding domain-1 pore tyrosine. J. Biol. Chem. 287, 28470–28479 (2012).
Iosefson, O., Olivares, A. O., Baker, T. A. & Sauer, R. T. Dissection of axial-pore loop operate throughout unfolding and translocation by a AAA+ proteolytic machine. Cell Rep. 12, 1032–1041 (2015).
Puchades, C., Sandate, C. R. & Lander, G. C. The molecular ideas governing the exercise and useful range of AAA+ proteins. Nat. Rev. Mol. Cell Biol. 21, 43–58 (2020).
Puchades, C. et al. Construction of the mitochondrial inside membrane AAA+ protease YME1 offers perception into substrate processing. Science 358, eaao0464 (2017).
Ripstein, Z. A., Huang, R., Augustyniak, R., Kay, L. E. & Rubinstein, J. L. Construction of a AAA+ unfoldase within the means of unfolding substrate. eLife 6, e25754 (2017).
Dong, Y. et al. Cryo-EM constructions and dynamics of substrate-engaged human 26S proteasome. Nature 565, 49–55 (2019).
Han, H. et al. Construction of Vps4 with round peptides and implications for translocation of two polypeptide chains by AAA+ ATPases. eLife 8, e44071 (2019).
Puchades, C. et al. Distinctive structural options of the mitochondrial AAA+ protease AFG3L2 reveal the molecular foundation for exercise in well being and illness. Mol. Cell 75, 1073–1085 (2019).
Fei, X. et al. Constructions of the ATP-fueled ClpXP proteolytic machine sure to protein substrate. eLife 9, e52774 (2020).
Fei, X., Bell, T. A., Barkow, S. R., Baker, T. A. & Sauer, R. T. Structural foundation of ClpXP recognition and unfolding of ssrA-tagged substrates. eLife 9, e61496 (2020).
Han, H. et al. Construction of spastin sure to a glutamate-rich peptide implies a hand-over-hand mechanism of substrate translocation. J. Biol. Chem. 295, 435–443 (2020).
Ripstein, Z. A., Vahidi, S., Houry, W. A., Rubinstein, J. L. & Kay, L. E. A processive rotary mechanism {couples} substrate unfolding and proteolysis within the ClpXP degradation equipment. eLife 9, e52158 (2020).
Krissinel, E. & Henrick, Okay. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774–797 (2007).
Hinnerwisch, J., Reid, B. G., Fenton, W. A. & Horwich, A. L. Roles of the N-domains of the ClpA unfoldase in binding substrate proteins and in secure advanced formation with the ClpP protease. J. Biol. Chem. 280, 40838–40844 (2005).
Singh, S. Okay., Grimaud, R., Hoskins, J. R., Wickner, S. & Maurizi, M. R. Unfolding and internalization of proteins by the ATP-dependent proteases ClpXP and ClpAP. Proc. Natl Acad. Sci. USA 97, 8898–8903 (2000).
Wang, Okay. H., Sauer, R. T. & Baker, T. A. ClpS modulates however is just not important for bacterial N-end rule degradation. Genes Dev. 21, 403–408 (2007).
Hoskins, J. R., Singh, S. Okay., Maurizi, M. R. & Wickner, S. Protein binding and unfolding by the chaperone ClpA and degradation by the protease ClpAP. Proc. Natl Acad. Sci. USA 97, 8892–8897 (2000).
Rivera-Rivera, I. Mechanism of Lively Substrate Supply by the AAA+ Protease Adaptor ClpS. PhD thesis, Massachusetts Institute of Know-how (2015); https://dspace.mit.edu/deal with/1721.1/101352
Barkow, S. R., Levchenko, I., Baker, T. A. & Sauer, R. T. Polypeptide translocation by the AAA+ ClpXP protease machine. Chem. Biol. 16, 605–612 (2009).
Bell, T. A., Baker, T. A. & Sauer, R. T. Interactions between a subset of substrate facet chains and AAA+ motor pore loops decide grip throughout protein unfolding. eLife 8, e46808 (2019).
Lin, L. & Ghosh, S. A glycine-rich area in NF-okB p105 features as a processing sign for the technology of the p50 subunit. Mol. Cell. Biol. 16, 2248–2254 (1996).
Levitskaya, J., Sharipo, A., Leonchiks, A., Ciechanover, A. & Masucci, M. G. Inhibition of ubiquitin/proteasome-dependent protein degradation by the Gly-Ala repeat area of the Epstein-Barr virus nuclear antigen 1. Proc. Natl Acad. Sci. USA 94, 12616–12621 (1997).
Sharipo, A., Imreh, M., Leonchiks, A., Brändén, C. I. & Masucci, M. G. cis-Inhibition of proteasomal degradation by viral repeats: impression of size and amino acid composition. FEBS Lett. 499, 137–142 (2001).
Hoyt, M. A. et al. Glycine-alanine repeats impair correct substrate unfolding by the proteasome. EMBO J. 25, 1720–1729 (2006).
Daskalogianni, C. et al. Gly-Ala repeats induce position- and substrate-specific regulation of 26S proteasome-dependent partial processing. J. Biol. Chem. 283, 30090–30100 (2008).
Kraut, D. A. et al. Sequence- and species-dependence of proteasomal processivity. ACS Chem. Biol. 7, 1444–1453 (2012).
Kraut, D. A. Slippery substrates impair ATP-dependent protease operate by slowing unfolding. J. Biol. Chem. 288, 34729–34735 (2013).
Too, P. H. M., Erales, J., Simen, J. D., Marjanovic, A. & Coffino, P. Slippery substrates impair operate of a bacterial protease ATPase by unbalancing translocation versus exit. J. Biol. Chem. 288, 13243–13257 (2013).
Vass, R. H. & Chien, P. Important clamp loader processing by a necessary AAA+ protease in Caulobacter crescentus. Proc. Natl Acad. Sci. USA 110, 18138–18143 (2013).
Yokom, A. L. et al. Spiral structure of the Hsp104 disaggregase reveals the premise for polypeptide translocation. Nat. Struct. Mol. Biol. 23, 830–837 (2016).
Johjima, A. et al. Microtubule severing by katanin p60 AAA+ ATPase requires the C-terminal acidic tails of each α- and β-tubulins and primary amino acid residues within the AAA+ ring pore. J. Biol. Chem. 290, 11762–11770 (2015).
Alfieri, C., Chang, L. & Barford, D. Mechanism for remodelling of the cell cycle checkpoint protein MAD2 by the ATPase TRIP13. Nature 559, 274–278 (2018).
Sandate, C. R., Szyk, A., Zehr, E. A., Lander, G. C. & Roll-Mecak, A. An allosteric community in spastin {couples} a number of actions required for microtubule severing. Nat. Struct. Mol. Biol. 26, 671–678 (2019).
Zehr, E. A., Szyk, A., Szczesna, E. & Roll-Mecak, A. Katanin grips the β-tubulin tail by an electropositive double spiral to sever microtubules. Dev. Cell 52, 118–131.e6 (2020).
Shin, M. et al. Constructions of the human LONP1 protease reveal regulatory steps concerned in protease activation. Nat. Commun. 12, 3239 (2021).
Kavalchuk, M., Jomaa, A., Müller, A. U. & Weber-Ban, E. Structural foundation of prokaryotic ubiquitin-like protein engagement and translocation by the mycobacterial Mpa–proteasome advanced. Nat. Commun. 13, 1–13 (2022).
Blok, N. B. et al. Distinctive double-ring construction of the peroxisomal Pex1/Pex6 ATPase advanced revealed by cryo-electron microscopy. Proc. Natl Acad. Sci. USA 112, E4017–E4025 (2015).
Gardner, B. M. et al. The peroxisomal AAA-ATPase Pex1/Pex6 unfolds substrates by processive threading. Nat. Commun. 9, 135 (2018).
Hattendorf, D. A. & Lindquist, S. L. Cooperative kinetics of each Hsp104 ATPase domains and interdomain communication revealed by AAA sensor-1 mutants. EMBO J. 21, 12–21 (2002).
Mogk, A. et al. Roles of particular person domains and conserved motifs of the AAA+ chaperone ClpB in oligomerization, ATP hydrolysis and chaperone exercise. J. Biol. Chem. 278, 17615–17624 (2003).
Wang, F. et al. Construction and mechanism of the hexameric MecA–ClpC molecular machine. Nature 471, 331–335 (2011).
Bodnar, N. & Rapoport, T. Towards an understanding of the Cdc48/p97 ATPase. F1000Res. 6, 1318 (2017).
Bodnar, N. O. & Rapoport, T. A. Molecular mechanism of substrate processing by the Cdc48 ATPase advanced. Cell 169, 722–735 (2017).
Edgar, R. C. MUSCLE: a number of sequence alignment with excessive accuracy and excessive throughput. Nucleic Acids Res. 32, 1792–1797 (2004).
Seol, J. H., Yoo, S. J., Kang, M.-S., Ha, D. B. & Chung, C. H. The 65-kDa protein derived from the interior translational begin website of the clpA gene blocks autodegradation of ClpA by the ATP-dependent protease Ti in Escherichia coli. FEBS Lett. 377, 41–43 (1995).
Kenniston, J. A., Baker, T. A., Fernandez, J. M. & Sauer, R. T. Linkage between ATP consumption and mechanical unfolding in the course of the protein processing reactions of an AAA+ degradation machine. Cell 114, 511–520 (2003).
Kim, Y. I., Burton, R. E., Burton, B. M., Sauer, R. T. & Baker, T. A. Dynamics of substrate denaturation and translocation by the ClpXP degradation machine. Mol. Cell 5, 639–648 (2000).
Nager, A. R., Baker, T. A. & Sauer, R. T. Stepwise unfolding of a β barrel protein by the AAA+ ClpXP protease. J. Mol. Biol. 413, 4–16 (2011).
Mastronarde, D. N. Automated electron microscope tomography utilizing sturdy prediction of specimen actions. J. Struct. Biol. 152, 36–51 (2005).
Zheng, S. Q. et al. MotionCor2: anisotropic correction of beam-induced movement for improved cryo-electron microscopy. Nat. Strategies 14, 331–332 (2017).
Rohou, A. & Grigorieff, N. CTFFIND4: quick and correct defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015).
Zivanov, J. et al. New instruments for automated high-resolution cryo-EM construction willpower in RELION-3. eLife 7, e42166 (2018).
Tan, Y. Z. et al. Addressing most popular specimen orientation in single-particle cryo-EM by tilting. Nat. Strategies 14, 793–796 (2017).
Adams, P. D. et al. PHENIX: a complete Python-based system for macromolecular construction answer. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).
Tang, G. et al. EMAN2: an extensible picture processing suite for electron microscopy. J. Struct. Biol. 157, 38–46 (2007).
Pettersen, E. F. et al. UCSF Chimera–a visualization system for exploratory analysis and evaluation. J. Comput. Chem. 25, 1605–1612 (2004).
Emsley, P. & Cowtan, Okay. Coot: model-building instruments for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004).
Williams, C. J. et al. MolProbity: extra and higher reference knowledge for improved all-atom construction validation. Protein Sci. 27, 293–315 (2018).
Barad, B. A. et al. EMRinger: facet chain-directed mannequin and map validation for 3D cryo-electron microscopy. Nat. Strategies 12, 943–946 (2015).
Pettersen, E. F. et al. UCSF ChimeraX: construction visualization for researchers, educators and builders. Protein Sci. 30, 70–82 (2021).
Bateman, A. et al. UniProt: the common protein knowledgebase in 2021. Nucleic Acids Res. 49, D480–D489 (2021).
Kumar, S., Stecher, G. & Tamura, Okay. MEGA7: Molecular Evolutionary Genetics Evaluation model 7.0 for larger datasets. Mol. Biol. Evol. 33, 1870–1874 (2016).
Waterhouse, A. M., Procter, J. B., Martin, D. M. A., Clamp, M. & Barton, G. J. Jalview Model 2–a a number of sequence alignment editor and evaluation workbench. Bioinformatics 25, 1189–1191 (2009).
Burton, R. E., Siddiqui, S. M., Kim, Y. I., Baker, T. A. & Sauer, R. T. Results of protein stability and construction on substrate processing by the ClpXP unfolding and degradation machine. EMBO J. 20, 3092–3100 (2001).