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Solution structure of the dimeric zinc binding domain of the chaperone ClpX.

Donaldson LW, Wojtyra U, Houry WA
J Biol Chem 278 48991-6 (2003)
Cited: 33 times
EuropePMC logo PMID: 14525985

Abstract

ClpX (423 amino acids), a member of the Clp/Hsp100 family of molecular chaperones and the protease, ClpP, comprise a multimeric complex supporting targeted protein degradation in Escherichia coli. The ClpX sequence consists of an NH2-terminal zinc binding domain (ZBD) and a COOH-terminal ATPase domain. Earlier, we have demonstrated that the zinc binding domain forms a constitutive dimer that is essential for the degradation of some ClpX substrates such as gammaO and MuA but is not required for the degradation of other substrates such as green fluorescent protein-SsrA. In this report, we present the NMR solution structure of the zinc binding domain dimer. The monomer fold reveals that ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions. However, the dimeric ZBD structure is not related to any protein structure in the Protein Data Bank. A trimer-of-dimers model of ZBD is presented, which might reflect the closed state of the ClpX hexamer.

Reviews - 1ovx mentioned but not cited (2)

  1. ClpXP, an ATP-powered unfolding and protein-degradation machine. Baker TA, Sauer RT. Biochim Biophys Acta 1823 15-28 (2012)
  2. Minimal Functional Sites in Metalloproteins and Their Usage in Structural Bioinformatics. Rosato A, Valasatava Y, Andreini C. Int J Mol Sci 17 E671 (2016)

Articles - 1ovx mentioned but not cited (4)

  1. Cryo-EM structure of the ClpXP protein degradation machinery. Gatsogiannis C, Balogh D, Merino F, Sieber SA, Raunser S. Nat Struct Mol Biol 26 946-954 (2019)
  2. Bhageerath: an energy based web enabled computer software suite for limiting the search space of tertiary structures of small globular proteins. Jayaram B, Bhushan K, Shenoy SR, Narang P, Bose S, Agrawal P, Sahu D, Pandey V. Nucleic Acids Res 34 6195-6204 (2006)
  3. Specificity in substrate and cofactor recognition by the N-terminal domain of the chaperone ClpX. Thibault G, Yudin J, Wong P, Tsitrin V, Sprangers R, Zhao R, Houry WA. Proc Natl Acad Sci U S A 103 17724-17729 (2006)
  4. Functional cooperativity between the trigger factor chaperone and the ClpXP proteolytic complex. Rizzolo K, Yu AYH, Ologbenla A, Kim SR, Zhu H, Ishimori K, Thibault G, Leung E, Zhang YW, Teng M, Haniszewski M, Miah N, Phanse S, Minic Z, Lee S, Caballero JD, Babu M, Tsai FTF, Saio T, Houry WA. Nat Commun 12 281 (2021)


Reviews citing this publication (8)

  1. AAA+ proteases: ATP-fueled machines of protein destruction. Sauer RT, Baker TA. Annu Rev Biochem 80 587-612 (2011)
  2. The power of two: protein dimerization in biology. Marianayagam NJ, Sunde M, Matthews JM. Trends Biochem Sci 29 618-625 (2004)
  3. Molecular machines for protein degradation. Groll M, Bochtler M, Brandstetter H, Clausen T, Huber R. Chembiochem 6 222-256 (2005)
  4. Protein binding and disruption by Clp/Hsp100 chaperones. Maurizi MR, Xia D. Structure 12 175-183 (2004)
  5. Mini review: ATP-dependent proteases in bacteria. Bittner LM, Arends J, Narberhaus F. Biopolymers 105 505-517 (2016)
  6. Chaperones and chaperone-substrate complexes: Dynamic playgrounds for NMR spectroscopists. Burmann BM, Hiller S. Prog Nucl Magn Reson Spectrosc 86-87 41-64 (2015)
  7. Recent structural insights into the mechanism of ClpP protease regulation by AAA+ chaperones and small molecules. Mabanglo MF, Houry WA. J Biol Chem 298 101781 (2022)
  8. Structure and function of ClpXP, a AAA+ proteolytic machine powered by probabilistic ATP hydrolysis. Sauer RT, Fei X, Bell TA, Baker TA. Crit Rev Biochem Mol Biol 57 188-204 (2022)

Articles citing this publication (19)

  1. Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine. Glynn SE, Martin A, Nager AR, Baker TA, Sauer RT. Cell 139 744-756 (2009)
  2. Molecular analysis of the Vibrio cholerae type II secretion ATPase EpsE. Camberg JL, Sandkvist M. J Bacteriol 187 249-256 (2005)
  3. Bivalent tethering of SspB to ClpXP is required for efficient substrate delivery: a protein-design study. Bolon DN, Wah DA, Hersch GL, Baker TA, Sauer RT. Mol Cell 13 443-449 (2004)
  4. Structural basis of SspB-tail recognition by the zinc binding domain of ClpX. Park EY, Lee BG, Hong SB, Kim HW, Jeon H, Song HK. J Mol Biol 367 514-526 (2007)
  5. Substrate recognition and processing by a Walker B mutant of the human mitochondrial AAA+ protein CLPX. Lowth BR, Kirstein-Miles J, Saiyed T, Brötz-Oesterhelt H, Morimoto RI, Truscott KN, Dougan DA. J Struct Biol 179 193-201 (2012)
  6. Roles of the N-domains of the ClpA unfoldase in binding substrate proteins and in stable complex formation with the ClpP protease. Hinnerwisch J, Reid BG, Fenton WA, Horwich AL. J Biol Chem 280 40838-40844 (2005)
  7. The ClpX and ClpP2 Orthologs of Chlamydia trachomatis Perform Discrete and Essential Functions in Organism Growth and Development. Wood NA, Blocker AM, Seleem MA, Conda-Sheridan M, Fisher DJ, Ouellette SP. mBio 11 e02016-20 (2020)
  8. Identification and characterization of a unique, zinc-containing transport ATPase essential for natural transformation in Thermus thermophilus HB27. Rose I, Biuković G, Aderhold P, Müller V, Grüber G, Averhoff B. Extremophiles 15 191-202 (2011)
  9. Large nucleotide-dependent movement of the N-terminal domain of the ClpX chaperone. Thibault G, Tsitrin Y, Davidson T, Gribun A, Houry WA. EMBO J 25 3367-3376 (2006)
  10. The flexible attachment of the N-domains to the ClpA ring body allows their use on demand. Cranz-Mileva S, Imkamp F, Kolygo K, Maglica Z, Kress W, Weber-Ban E. J Mol Biol 378 412-424 (2008)
  11. The N-terminal coiled coil of the Rhodococcus erythropolis ARC AAA ATPase is neither necessary for oligomerization nor nucleotide hydrolysis. Zhang X, Stoffels K, Wurzbacher S, Schoofs G, Pfeifer G, Banerjee T, Parret AH, Baumeister W, De Mot R, Zwickl P. J Struct Biol 146 155-165 (2004)
  12. Versatile modes of peptide recognition by the ClpX N domain mediate alternative adaptor-binding specificities in different bacterial species. Chowdhury T, Chien P, Ebrahim S, Sauer RT, Baker TA. Protein Sci 19 242-254 (2010)
  13. New insights into structural and functional relationships between LonA proteases and ClpB chaperones. Rotanova TV, Andrianova AG, Kudzhaev AM, Li M, Botos I, Wlodawer A, Gustchina A. FEBS Open Bio 9 1536-1551 (2019)
  14. Structural and Functional Insights into Bacillus subtilis Sigma Factor Inhibitor, CsfB. Martínez-Lumbreras S, Alfano C, Evans NJ, Collins KM, Flanagan KA, Atkinson RA, Krysztofinska EM, Vydyanath A, Jackter J, Fixon-Owoo S, Camp AH, Isaacson RL. Structure 26 640-648.e5 (2018)
  15. A degradation signal recognition in prokaryotes. Park EY, Song HK. J Synchrotron Radiat 15 246-249 (2008)
  16. ClpP-independent function of ClpX interferes with telithromycin resistance conferred by Msr(A) in Staphylococcus aureus. Vimberg V, Lenart J, Janata J, Balikova Novotna G. Antimicrob Agents Chemother 59 3611-3614 (2015)
  17. Degradation of the E. coli antitoxin MqsA by the proteolytic complex ClpXP is regulated by zinc occupancy and oxidation. Vos MR, Piraino B, LaBreck CJ, Rahmani N, Trebino CE, Schoenle M, Peti W, Camberg JL, Page R. J Biol Chem 298 101557 (2022)
  18. Deciphering the mechanism and function of Hsp100 unfoldases from protein structure. Lee G, Kim RS, Lee SB, Lee S, Tsai FTF. Biochem Soc Trans 50 1725-1736 (2022)
  19. Selectivity among Anti-σ Factors by Mycobacterium tuberculosis ClpX Influences Intracellular Levels of Extracytoplasmic Function σ Factors. Joshi AC, Kaur P, Nair RK, Lele DS, Nandicoori VK, Gopal B. J Bacteriol 201 e00748-18 (2019)


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