PDBsum entry 1tyf

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protein Protein-protein interface(s) links
Peptidase PDB id
Protein chains
(+ 8 more) 183 a.a. *
Waters ×1246
* Residue conservation analysis
PDB id:
Name: Peptidase
Title: The structure of clpp at 2.3 angstrom resolution suggests a model for atp-dependent proteolysis
Structure: Clp peptidase. Chain: a, b, c, d, e, f, g, h, i, j, k, l, m, n. Synonym: clpp. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562
Biol. unit: 40mer (from PQS)
2.30Å     R-factor:   0.219     R-free:   0.292
Authors: J.Wang,J.A.Hartling,J.M.Flanagan
Key ref:
J.Wang et al. (1997). The structure of ClpP at 2.3 A resolution suggests a model for ATP-dependent proteolysis. Cell, 91, 447-456. PubMed id: 9390554 DOI: 10.1016/S0092-8674(00)80431-6
13-Oct-97     Release date:   17-Jun-98    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P0A6G7  (CLPP_ECOLI) -  ATP-dependent Clp protease proteolytic subunit
207 a.a.
183 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Endopeptidase Clp.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of proteins to small peptides in the presence of ATP and magnesium. Alpha-casein is the usual test substrate. In the absence of ATP, only oligopeptides shorter than five residues are cleaved (such as succinyl-Leu-Tyr-|-NHMEC; and Leu-Tyr-Leu-|-Tyr-Trp, in which the cleavage of the -Tyr-|-Leu- and -Tyr-|-Trp- bond also occurs).
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   3 terms 
  Biological process     response to stress   5 terms 
  Biochemical function     hydrolase activity     5 terms  


DOI no: 10.1016/S0092-8674(00)80431-6 Cell 91:447-456 (1997)
PubMed id: 9390554  
The structure of ClpP at 2.3 A resolution suggests a model for ATP-dependent proteolysis.
J.Wang, J.A.Hartling, J.M.Flanagan.
We have determined the crystal structure of the proteolytic component of the caseinolytic Clp protease (ClpP) from E. coli at 2.3 A resolution using an ab initio phasing procedure that exploits the internal 14-fold symmetry of the oligomer. The structure of a ClpP monomer has a distinct fold that defines a fifth structural family of serine proteases but a conserved catalytic apparatus. The active protease resembles a hollow, solid-walled cylinder composed of two 7-fold symmetric rings stacked back-to-back. Its 14 proteolytic active sites are located within a central, roughly spherical chamber approximately 51 A in diameter. Access to the proteolytic chamber is controlled by two axial pores, each having a minimum diameter of approximately 10 A. From the structural features of ClpP, we suggest a model for its action in degrading proteins.
  Selected figure(s)  
Figure 1.
Figure 1. Electron Density Map of the Region between Helix C and Strand 5The |F[o]|exp(iφ^ave) electron density map is contoured at 1.5 σ and superimposed upon the refined model. |Fo| and φ^ave are the observed amplitudes, and the calculated phases after NCS averaging with RAVE ([23]), respectively. In this map, the turn between helix C and strand 5 (residues 80–85) is stabilized by a solvent molecule or a cation. The refined model is superimposed on the density as a wire model. A water molecule and the unidentified solvent/cation molecule are shown as magenta spheres.
Figure 5.
Figure 5. Subunit Interface in ClpP(A) The intra-ring association of ClpP monomers is shown as a ribbon diagram. Monomer 1 is shown in gray, monomer 2 in olive; residues in the catalytic triad and those that stabilize the oxyanion intermediate are represented as spheres: Ser-97 is magenta, His-122 is green, Asp-171 is red, and Gly-68 and Met-98 are olive. Dimerization of the two rings of heptamers results in the formation of an antiparallel β sheet comprising strand 9 from two NCS-related subunits. The small (+) represents the two-fold axis relating the stacked monomers in opposing rings.(B) The intraring contacts between monomers are shown; in one ring, monomer 1 (gray) in (A) packs against monomer 3 shown in blue, and in the opposing ring, monomer 2 (olive) in (A) packs against monomer 4 shown in cyan. As in (A), the catalytic residues are shown as spheres. As in (A), the small (+) represents the location of the two-fold axis relating stacked monomers; the large (+) represents the location of a second two-fold axis that lies between each pair of interring subunits.(C) A CPK representation of (B) showing the interdigitation of the monomers.(D) A solvent-accessible surface representation of (B) shows the connection between adjacent active site clefts in the heptameric ring. The active sites in opposing heptamers are also connected by channels that lie along the two-fold axes of the oligomer, giving the surface of the proteolytic chamber a zigzag-like appearance.(E) A schematic representation of two putative models of substrate binding. Strands 9 are drawn as unshaded arrows and heptapeptides as shaded arrows. Dashed lines represent possible connections between hepta-peptides in a continuous substrate. Residues in the catalytic triads are drawn as spheres.(F) A longitudinal section of a space-filling model colored according to hydrophobicity. The apical and outer equatorial surfaces are enriched in charged residues, whereas the inner surface of the chamber is largely hydrophobic. In this representation, hydrophobic residues (Tyr, Phe, Leu, Ile, Met, Val, Pro, and Ala) are colored in yellow, while charged residues are colored in blue (Lys and Arg) and red (Asp and Glu), respectively. All other residues are colored in gray.
  The above figures are reprinted by permission from Cell Press: Cell (1997, 91, 447-456) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21247409 H.Schuhmann, U.Mogg, and I.Adamska (2011).
A new principle of oligomerization of plant DEG7 protease based on interactions of degenerated protease domains.
  Biochem J, 435, 167-174.  
21265751 M.Krupovic, A.Spang, S.Gribaldo, P.Forterre, and C.Schleper (2011).
A thaumarchaeal provirus testifies for an ancient association of tailed viruses with archaea.
  Biochem Soc Trans, 39, 82-88.  
21529717 R.A.Maillard, G.Chistol, M.Sen, M.Righini, J.Tan, C.M.Kaiser, C.Hodges, A.Martin, and C.Bustamante (2011).
ClpX(P) Generates Mechanical Force to Unfold and Translocate Its Protein Substrates.
  Cell, 145, 459-469.  
20502673 A.Stein, and P.Aloy (2010).
Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures.
  PLoS Comput Biol, 6, e1000789.  
  20975890 A.Tiwari, S.Gupta, S.Srivastava, R.Srivastava, and A.K.Rawat (2010).
A ClpP protein model as tuberculosis target for screening marine compounds.
  Bioinformation, 4, 405-408.  
20851345 D.H.Li, Y.S.Chung, M.Gloyd, E.Joseph, R.Ghirlando, G.D.Wright, Y.Q.Cheng, M.R.Maurizi, A.Guarné, and J.Ortega (2010).
Acyldepsipeptide antibiotics induce the formation of a structured axial channel in ClpP: A model for the ClpX/ClpA-bound state of ClpP.
  Chem Biol, 17, 959-969.
PDB code: 3mt6
20388215 D.S.Ow, D.Y.Lim, P.M.Nissom, A.Camattari, and V.V.Wong (2010).
Co-expression of Skp and FkpA chaperones improves cell viability and alters the global expression of stress response genes during scFvD1.3 production.
  Microb Cell Fact, 9, 22.  
20633347 D.Sheppard, R.Sprangers, and V.Tugarinov (2010).
Experimental approaches for NMR studies of side-chain dynamics in high-molecular-weight proteins.
  Prog Nucl Magn Reson Spectrosc, 56, 1.  
  20936072 J.N.Ollivierre, J.Fang, and P.J.Beuning (2010).
The Roles of UmuD in Regulating Mutagenesis.
  J Nucleic Acids, 2010, 0.  
20637416 M.S.Kimber, A.Y.Yu, M.Borg, E.Leung, H.S.Chan, and W.A.Houry (2010).
Structural and theoretical studies indicate that the cylindrical protease ClpP samples extended and compact conformations.
  Structure, 18, 798-808.
PDB code: 3hln
20038588 P.Chattoraj, A.Banerjee, S.Biswas, and I.Biswas (2010).
ClpP of Streptococcus mutans differentially regulates expression of genomic islands, mutacin production, and antibiotic tolerance.
  J Bacteriol, 192, 1312-1323.  
20834233 S.S.Cha, Y.J.An, C.R.Lee, H.S.Lee, Y.G.Kim, S.J.Kim, K.K.Kwon, G.M.De Donatis, J.H.Lee, M.R.Maurizi, and S.G.Kang (2010).
Crystal structure of Lon protease: molecular architecture of gated entry to a sequestered degradation chamber.
  EMBO J, 29, 3520-3530.
PDB code: 3k1j
20014030 T.Chowdhury, P.Chien, S.Ebrahim, R.T.Sauer, and T.A.Baker (2010).
Versatile modes of peptide recognition by the ClpX N domain mediate alternative adaptor-binding specificities in different bacterial species.
  Protein Sci, 19, 242-254.  
20167127 X.H.Li, Y.L.Zeng, Y.Gao, X.C.Zheng, Q.F.Zhang, S.N.Zhou, and Y.J.Lu (2010).
The ClpP protease homologue is required for the transmission traits and cell division of the pathogen Legionella pneumophila.
  BMC Microbiol, 10, 54.  
19846313 A.K.Mittermaier, and L.E.Kay (2009).
Observing biological dynamics at atomic resolution using NMR.
  Trends Biochem Sci, 34, 601-611.  
19346247 B.Derrien, W.Majeran, F.A.Wollman, and O.Vallon (2009).
Multistep processing of an insertion sequence in an essential subunit of the chloroplast ClpP complex.
  J Biol Chem, 284, 15408-15415.  
19654317 D.Kress, D.Brügel, I.Schall, D.Linder, W.Buckel, and L.O.Essen (2009).
An asymmetric model for Na+-translocating glutaconyl-CoA decarboxylases.
  J Biol Chem, 284, 28401-28409.
PDB codes: 3gf3 3gf7 3glm 3gma
19237538 F.I.Andersson, A.Tryggvesson, M.Sharon, A.V.Diemand, M.Classen, C.Best, R.Schmidt, J.Schelin, T.M.Stanne, B.Bukau, C.V.Robinson, S.Witt, A.Mogk, and A.K.Clarke (2009).
Structure and Function of a Novel Type of ATP-dependent Clp Protease.
  J Biol Chem, 284, 13519-13532.  
19541655 J.L.Camberg, J.R.Hoskins, and S.Wickner (2009).
ClpXP protease degrades the cytoskeletal protein, FtsZ, and modulates FtsZ polymer dynamics.
  Proc Natl Acad Sci U S A, 106, 10614-10619.  
19047352 J.Zhang, A.Banerjee, and I.Biswas (2009).
Transcription of clpP is enhanced by a unique tandem repeat sequence in Streptococcus mutans.
  J Bacteriol, 191, 1056-1065.  
19317833 R.Schmidt, R.Zahn, B.Bukau, and A.Mogk (2009).
ClpS is the recognition component for Escherichia coli substrates of the N-end rule degradation pathway.
  Mol Microbiol, 72, 506-517.  
19914167 S.E.Glynn, A.Martin, A.R.Nager, T.A.Baker, and R.T.Sauer (2009).
Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine.
  Cell, 139, 744-756.
PDB codes: 3hte 3hws
19368879 S.G.Burston (2009).
Anything a ClpA can do, two ClpAs can do better.
  Structure, 17, 483-484.  
19549599 S.R.Barkow, I.Levchenko, T.A.Baker, and R.T.Sauer (2009).
Polypeptide translocation by the AAA+ ClpXP protease machine.
  Chem Biol, 16, 605-612.  
19892734 Y.Shin, J.H.Davis, R.R.Brau, A.Martin, J.A.Kenniston, T.A.Baker, R.T.Sauer, and M.J.Lang (2009).
Single-molecule denaturation and degradation of proteins by the AAA+ ClpXP protease.
  Proc Natl Acad Sci U S A, 106, 19340-19345.  
19368884 Z.Maglica, K.Kolygo, and E.Weber-Ban (2009).
Optimal efficiency of ClpAP and ClpXP chaperone-proteases is achieved by architectural symmetry.
  Structure, 17, 508-516.  
18818204 A.Karradt, J.Sobanski, J.Mattow, W.Lockau, and K.Baier (2008).
NblA, a Key Protein of Phycobilisome Degradation, Interacts with ClpC, a HSP100 Chaperone Partner of a Cyanobacterial Clp Protease.
  J Biol Chem, 283, 32394-32403.  
18421152 H.Yokoyama, S.Hamamatsu, S.Fujii, and I.Matsui (2008).
Novel dimer structure of a membrane-bound protease with a catalytic Ser-Lys dyad and its linkage to stomatin.
  J Synchrotron Radiat, 15, 254-257.
PDB code: 3bpp
18582897 J.A.Yakamavich, T.A.Baker, and R.T.Sauer (2008).
Asymmetric nucleotide transactions of the HslUV protease.
  J Mol Biol, 380, 946-957.  
18682217 J.Bohon, L.D.Jennings, C.M.Phillips, S.Licht, and M.R.Chance (2008).
Synchrotron protein footprinting supports substrate translocation by ClpA via ATP-induced movements of the D2 loop.
  Structure, 16, 1157-1165.  
18394159 J.C.Zweers, I.Barák, D.Becher, A.J.Driessen, M.Hecker, V.P.Kontinen, M.J.Saller, L.Vavrová, and J.M.van Dijl (2008).
Towards the development of Bacillus subtilis as a cell factory for membrane proteins and protein complexes.
  Microb Cell Fact, 7, 10.  
18550545 K.H.Wang, E.S.Oakes, R.T.Sauer, and T.A.Baker (2008).
Tuning the Strength of a Bacterial N-end Rule Degradation Signal.
  J Biol Chem, 283, 24600-24607.  
18230617 K.R.Marshall-Batty, and H.Nakai (2008).
Activation of a dormant ClpX recognition motif of bacteriophage Mu repressor by inducing high local flexibility.
  J Biol Chem, 283, 9060-9070.  
18816064 L.D.Jennings, J.Bohon, M.R.Chance, and S.Licht (2008).
The ClpP N-terminus coordinates substrate access with protease active site reactivity.
  Biochemistry, 47, 11031-11040.  
18824507 O.D.Ekici, M.Paetzel, and R.E.Dalbey (2008).
Unconventional serine proteases: variations on the catalytic Ser/His/Asp triad configuration.
  Protein Sci, 17, 2023-2037.  
17979190 S.H.Rho, H.H.Park, G.B.Kang, Y.J.Im, M.S.Kang, B.K.Lim, I.S.Seong, J.Seol, C.H.Chung, J.Wang, and S.H.Eom (2008).
Crystal structure of Bacillus subtilis CodW, a noncanonical HslV-like peptidase with an impaired catalytic apparatus.
  Proteins, 71, 1020-1026.
PDB codes: 2z3a 2z3b
18505836 T.Krojer, K.Pangerl, J.Kurt, J.Sawa, C.Stingl, K.Mechtler, R.Huber, M.Ehrmann, and T.Clausen (2008).
Interplay of PDZ and protease domain of DegP ensures efficient elimination of misfolded proteins.
  Proc Natl Acad Sci U S A, 105, 7702-7707.  
17981983 U.Gerth, H.Kock, I.Kusters, S.Michalik, R.L.Switzer, and M.Hecker (2008).
Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis.
  J Bacteriol, 190, 321-331.  
18723625 Y.Chang, G.E.Wesenberg, C.A.Bingman, and B.G.Fox (2008).
In vivo inactivation of the mycobacterial integral membrane stearoyl coenzyme A desaturase DesA3 by a C-terminus-specific degradation process.
  J Bacteriol, 190, 6686-6696.  
17612489 A.Martin, T.A.Baker, and R.T.Sauer (2007).
Distinct static and dynamic interactions control ATPase-peptidase communication in a AAA+ protease.
  Mol Cell, 27, 41-52.  
17302811 D.Frees, K.Savijoki, P.Varmanen, and H.Ingmer (2007).
Clp ATPases and ClpP proteolytic complexes regulate vital biological processes in low GC, Gram-positive bacteria.
  Mol Microbiol, 63, 1285-1295.  
17241447 G.Shen, J.Yan, V.Pasapula, J.Luo, C.He, A.K.Clarke, and H.Zhang (2007).
The chloroplast protease subunit ClpP4 is a substrate of the E3 ligase AtCHIP and plays an important role in chloroplast function.
  Plant J, 49, 228-237.  
17242518 H.Ingvarsson, M.J.Maté, M.Högbom, D.Portnoï, N.Benaroudj, P.M.Alzari, M.Ortiz-Lombardía, and T.Unge (2007).
Insights into the inter-ring plasticity of caseinolytic proteases from the X-ray structure of Mycobacterium tuberculosis ClpP1.
  Acta Crystallogr D Biol Crystallogr, 63, 249-259.
PDB codes: 2c8t 2cby 2ce3
17933920 M.T.Cohn, H.Ingmer, F.Mulholland, K.Jørgensen, J.M.Wells, and L.Brøndsted (2007).
Contribution of conserved ATP-dependent proteases of Campylobacter jejuni to stress tolerance and virulence.
  Appl Environ Microbiol, 73, 7803-7813.  
17039546 N.Nagano, T.Noguchi, and Y.Akiyama (2007).
Systematic comparison of catalytic mechanisms of hydrolysis and transfer reactions classified in the EzCatDB database.
  Proteins, 66, 147-159.  
17420450 P.Chien, B.S.Perchuk, M.T.Laub, R.T.Sauer, and T.A.Baker (2007).
Direct and adaptor-mediated substrate recognition by an essential AAA+ protease.
  Proc Natl Acad Sci U S A, 104, 6590-6595.  
17762877 R.Sprangers, A.Velyvis, and L.E.Kay (2007).
Solution NMR of supramolecular complexes: providing new insights into function.
  Nat Methods, 4, 697-703.  
17009084 S.Koussevitzky, T.M.Stanne, C.A.Peto, T.Giap, L.L.Sjögren, Y.Zhao, A.K.Clarke, and J.Chory (2007).
An Arabidopsis thaliana virescent mutant reveals a role for ClpR1 in plastid development.
  Plant Mol Biol, 63, 85-96.  
17371875 T.M.Stanne, E.Pojidaeva, F.I.Andersson, and A.K.Clarke (2007).
Distinctive types of ATP-dependent Clp proteases in cyanobacteria.
  J Biol Chem, 282, 14394-14402.  
16902918 B.Hinzen, S.Raddatz, H.Paulsen, T.Lampe, A.Schumacher, D.Häbich, V.Hellwig, J.Benet-Buchholz, R.Endermann, H.Labischinski, and H.Brötz-Oesterhelt (2006).
Medicinal chemistry optimization of acyldepsipeptides of the enopeptin class antibiotics.
  ChemMedChem, 1, 689-693.  
16705403 B.Zheng, T.M.MacDonald, S.Sutinen, V.Hurry, and A.K.Clarke (2006).
A nuclear-encoded ClpP subunit of the chloroplast ATP-dependent Clp protease is essential for early development in Arabidopsis thaliana.
  Planta, 224, 1103-1115.  
16672233 E.J.Miller, A.S.Meyer, and J.Frydman (2006).
Modeling of possible subunit arrangements in the eukaryotic chaperonin TRiC.
  Protein Sci, 15, 1522-1526.  
16881035 F.von Nussbaum, M.Brands, B.Hinzen, S.Weigand, and D.Häbich (2006).
Antibacterial natural products in medicinal chemistry--exodus or revival?
  Angew Chem Int Ed Engl, 45, 5072-5129.  
16973604 G.Schoehn, F.M.Vellieux, M.Asunción Durá, V.Receveur-Bréchot, C.M.Fabry, R.W.Ruigrok, C.Ebel, A.Roussel, and B.Franzetti (2006).
An archaeal peptidase assembles into two different quaternary structures: A tetrahedron and a giant octahedron.
  J Biol Chem, 281, 36327-36337.
PDB code: 2cf4
17090685 G.Thibault, J.Yudin, P.Wong, V.Tsitrin, R.Sprangers, R.Zhao, and W.A.Houry (2006).
Specificity in substrate and cofactor recognition by the N-terminal domain of the chaperone ClpX.
  Proc Natl Acad Sci U S A, 103, 17724-17729.  
16810315 G.Thibault, Y.Tsitrin, T.Davidson, A.Gribun, and W.A.Houry (2006).
Large nucleotide-dependent movement of the N-terminal domain of the ClpX chaperone.
  EMBO J, 25, 3367-3376.  
16525504 J.Kirstein, T.Schlothauer, D.A.Dougan, H.Lilie, G.Tischendorf, A.Mogk, B.Bukau, and K.Turgay (2006).
Adaptor protein controlled oligomerization activates the AAA+ protein ClpC.
  EMBO J, 25, 1481-1491.  
17181860 M.García-Lorenzo, A.Sjödin, S.Jansson, and C.Funk (2006).
Protease gene families in Populus and Arabidopsis.
  BMC Plant Biol, 6, 30.  
16911042 M.Ventura, C.Canchaya, Z.Zhang, V.Bernini, G.F.Fitzgerald, and D.van Sinderen (2006).
How high G+C Gram-positive bacteria and in particular bifidobacteria cope with heat stress: protein players and regulators.
  FEMS Microbiol Rev, 30, 734-759.  
16438678 R.E.De Castro, J.A.Maupin-Furlow, M.I.Giménez, M.K.Herrera Seitz, and J.J.Sánchez (2006).
Haloarchaeal proteases and proteolytic systems.
  FEMS Microbiol Rev, 30, 17-35.  
16762831 R.Suno, H.Niwa, D.Tsuchiya, X.Zhang, M.Yoshida, and K.Morikawa (2006).
Structure of the whole cytosolic region of ATP-dependent protease FtsH.
  Mol Cell, 22, 575-585.
PDB codes: 2dhr 2di4 4eiw
17038198 S.Fico, and J.Mahillon (2006).
TasA-tasB, a new putative toxin-antitoxin (TA) system from Bacillus thuringiensis pGI1 plasmid is a widely distributed composite mazE-doc TA system.
  BMC Genomics, 7, 259.  
16788195 S.J.Pamp, D.Frees, S.Engelmann, M.Hecker, and H.Ingmer (2006).
Spx is a global effector impacting stress tolerance and biofilm formation in Staphylococcus aureus.
  J Bacteriol, 188, 4861-4870.  
16629660 S.M.Butler, R.A.Festa, M.J.Pearce, and K.H.Darwin (2006).
Self-compartmentalized bacterial proteases and pathogenesis.
  Mol Microbiol, 60, 553-562.  
16483314 T.Okuno, K.Yamanaka, and T.Ogura (2006).
An AAA protease FtsH can initiate proteolysis from internal sites of a model substrate, apo-flavodoxin.
  Genes Cells, 11, 261-268.  
16877706 T.V.Rotanova, I.Botos, E.E.Melnikov, F.Rasulova, A.Gustchina, M.R.Maurizi, and A.Wlodawer (2006).
Slicing a protease: structural features of the ATP-dependent Lon proteases gleaned from investigations of isolated domains.
  Protein Sci, 15, 1815-1828.  
16669775 W.Sakamoto (2006).
Protein degradation machineries in plastids.
  Annu Rev Plant Biol, 57, 599-621.  
15701650 A.Gribun, M.S.Kimber, R.Ching, R.Sprangers, K.M.Fiebig, and W.A.Houry (2005).
The ClpP double ring tetradecameric protease exhibits plastic ring-ring interactions, and the N termini of its subunits form flexible loops that are essential for ClpXP and ClpAP complex formation.
  J Biol Chem, 280, 16185-16196.
PDB code: 1y7o
16046622 B.M.Burton, and T.A.Baker (2005).
Remodeling protein complexes: insights from the AAA+ unfoldase ClpX and Mu transposase.
  Protein Sci, 14, 1945-1954.  
16299304 D.Frees, K.Sørensen, and H.Ingmer (2005).
Global virulence regulation in Staphylococcus aureus: pinpointing the roles of ClpP and ClpX in the sar/agr regulatory network.
  Infect Immun, 73, 8100-8108.  
15843987 D.Frees, L.E.Thomsen, and H.Ingmer (2005).
Staphylococcus aureus ClpYQ plays a minor role in stress survival.
  Arch Microbiol, 183, 286-291.  
15989952 G.L.Hersch, R.E.Burton, D.N.Bolon, T.A.Baker, and R.T.Sauer (2005).
Asymmetric interactions of ATP with the AAA+ ClpX6 unfoldase: allosteric control of a protein machine.
  Cell, 121, 1017-1027.  
15657062 G.Piszczek, J.Rozycki, S.K.Singh, A.Ginsburg, and M.R.Maurizi (2005).
The molecular chaperone, ClpA, has a single high affinity peptide binding site per hexamer.
  J Biol Chem, 280, 12221-12230.  
16200071 H.Brötz-Oesterhelt, D.Beyer, H.P.Kroll, R.Endermann, C.Ladel, W.Schroeder, B.Hinzen, S.Raddatz, H.Paulsen, K.Henninger, J.E.Bandow, H.G.Sahl, and H.Labischinski (2005).
Dysregulation of bacterial proteolytic machinery by a new class of antibiotics.
  Nat Med, 11, 1082-1087.  
15880122 I.Levchenko, R.A.Grant, J.M.Flynn, R.T.Sauer, and T.A.Baker (2005).
Versatile modes of peptide recognition by the AAA+ adaptor protein SspB.
  Nat Struct Mol Biol, 12, 520-525.
PDB code: 1yfn
16211032 J.S.Blanchard (2005).
Old approach yields new antibiotic.
  Nat Med, 11, 1045-1046.  
15584023 N.Zamboni, E.Fischer, A.Muffler, M.Wyss, H.P.Hohmann, and U.Sauer (2005).
Transient expression and flux changes during a shift from high to low riboflavin production in continuous cultures of Bacillus subtilis.
  Biotechnol Bioeng, 89, 219-232.  
16072036 P.I.Hanson, and S.W.Whiteheart (2005).
AAA+ proteins: have engine, will work.
  Nat Rev Mol Cell Biol, 6, 519-529.  
16263929 R.Sprangers, A.Gribun, P.M.Hwang, W.A.Houry, and L.E.Kay (2005).
Quantitative NMR spectroscopy of supramolecular complexes: dynamic side pores in ClpP are important for product release.
  Proc Natl Acad Sci U S A, 102, 16678-16683.  
16115876 S.G.Kang, M.N.Dimitrova, J.Ortega, A.Ginsburg, and M.R.Maurizi (2005).
Human mitochondrial ClpP is a stable heptamer that assembles into a tetradecamer in the presence of ClpX.
  J Biol Chem, 280, 35424-35432.  
15591068 S.Sharma, J.R.Hoskins, and S.Wickner (2005).
Binding and degradation of heterodimeric substrates by ClpAP and ClpXP.
  J Biol Chem, 280, 5449-5455.  
16262695 W.Majeran, G.Friso, K.J.van Wijk, and O.Vallon (2005).
The chloroplast ClpP complex in Chlamydomonas reinhardtii contains an unusual high molecular mass subunit with a large apical domain.
  FEBS J, 272, 5558-5571.  
15028706 C.Beltramo, C.Grandvalet, F.Pierre, and J.Guzzo (2004).
Evidence for multiple levels of regulation of Oenococcus oeni clpP-clpL locus expression in response to stress.
  J Bacteriol, 186, 2200-2205.  
14990998 C.M.Pickart, and R.E.Cohen (2004).
Proteasomes and their kin: proteases in the machine age.
  Nat Rev Mol Cell Biol, 5, 177-187.  
15525508 D.N.Bolon, R.A.Grant, T.A.Baker, and R.T.Sauer (2004).
Nucleotide-dependent substrate handoff from the SspB adaptor to the AAA+ ClpXP protease.
  Mol Cell, 16, 343-350.
PDB code: 1twb
15273316 H.Cheng, N.Shen, J.Pei, and N.V.Grishin (2004).
Double-stranded DNA bacteriophage prohead protease is homologous to herpesvirus protease.
  Protein Sci, 13, 2260-2269.  
14665623 I.Botos, E.E.Melnikov, S.Cherry, J.E.Tropea, A.G.Khalatova, F.Rasulova, Z.Dauter, M.R.Maurizi, T.V.Rotanova, A.Wlodawer, and A.Gustchina (2004).
The catalytic domain of Escherichia coli Lon protease has a unique fold and a Ser-Lys dyad in the active site.
  J Biol Chem, 279, 8140-8148.
PDB codes: 1rr9 1rre
14593120 J.B.Peltier, D.R.Ripoll, G.Friso, A.Rudella, Y.Cai, J.Ytterberg, L.Giacomelli, J.Pillardy, and K.J.van Wijk (2004).
Clp protease complexes from photosynthetic and non-photosynthetic plastids and mitochondria of plants, their predicted three-dimensional structures, and functional implications.
  J Biol Chem, 279, 4768-4781.
PDB codes: 1r8v 1r8z 1r90 1r91 1r92 1r93 1r96 1r97 1r98 1r99 1r9a 1r9b
15205439 J.Liu, and A.Mushegian (2004).
Displacements of prohead protease genes in the late operons of double-stranded-DNA bacteriophages.
  J Bacteriol, 186, 4369-4375.  
15371343 J.M.Flynn, I.Levchenko, R.T.Sauer, and T.A.Baker (2004).
Modulating substrate choice: the SspB adaptor delivers a regulator of the extracytoplasmic-stress response to the AAA+ protease ClpXP for degradation.
  Genes Dev, 18, 2292-2301.  
15454077 R.T.Sauer, D.N.Bolon, B.M.Burton, R.E.Burton, J.M.Flynn, R.A.Grant, G.L.Hersch, S.A.Joshi, J.A.Kenniston, I.Levchenko, S.B.Neher, E.S.Oakes, S.M.Siddiqui, D.A.Wah, and T.A.Baker (2004).
Sculpting the proteome with AAA(+) proteases and disassembly machines.
  Cell, 119, 9.  
15064753 S.A.Joshi, G.L.Hersch, T.A.Baker, and R.T.Sauer (2004).
Communication between ClpX and ClpP during substrate processing and degradation.
  Nat Struct Mol Biol, 11, 404-411.  
15175655 S.Hutschenreiter, A.Tinazli, K.Model, and R.Tampé (2004).
Two-substrate association with the 20S proteasome at single-molecule level.
  EMBO J, 23, 2488-2497.  
15004005 S.M.Siddiqui, R.T.Sauer, and T.A.Baker (2004).
Role of the processing pore of the ClpX AAA+ ATPase in the recognition and engagement of specific protein substrates.
  Genes Dev, 18, 369-374.  
14679237 U.Gerth, J.Kirstein, J.Mostertz, T.Waldminghaus, M.Miethke, H.Kock, and M.Hecker (2004).
Fine-tuning in regulation of Clp protein content in Bacillus subtilis.
  J Bacteriol, 186, 179-191.  
15189138 V.Tugarinov, P.M.Hwang, and L.E.Kay (2004).
Nuclear magnetic resonance spectroscopy of high-molecular-weight proteins.
  Annu Rev Biochem, 73, 107-146.  
15456757 Y.J.Im, Y.Na, G.B.Kang, S.H.Rho, M.K.Kim, J.H.Lee, C.H.Chung, and S.H.Eom (2004).
The active site of a lon protease from Methanococcus jannaschii distinctly differs from the canonical catalytic Dyad of Lon proteases.
  J Biol Chem, 279, 53451-53457.
PDB code: 1xhk
12581666 A.Matouschek (2003).
Protein unfolding--an important process in vivo?
  Curr Opin Struct Biol, 13, 98.  
12770828 B.M.Burton, and T.A.Baker (2003).
Mu transpososome architecture ensures that unfolding by ClpX or proteolysis by ClpXP remodels but does not destroy the complex.
  Chem Biol, 10, 463-472.  
12791139 D.Frees, S.N.Qazi, P.J.Hill, and H.Ingmer (2003).
Alternative roles of ClpX and ClpP in Staphylococcus aureus stress tolerance and virulence.
  Mol Microbiol, 48, 1565-1578.  
12458220 D.Y.Kim, D.R.Kim, S.C.Ha, N.K.Lokanath, C.J.Lee, H.Y.Hwang, and K.K.Kim (2003).
Crystal structure of the protease domain of a heat-shock protein HtrA from Thermotoga maritima.
  J Biol Chem, 278, 6543-6551.
PDB code: 1l1j
14514695 D.Y.Kim, and K.K.Kim (2003).
Crystal structure of ClpX molecular chaperone from Helicobacter pylori.
  J Biol Chem, 278, 50664-50670.
PDB code: 1um8
12887894 H.K.Song, and M.J.Eck (2003).
Structural basis of degradation signal recognition by SspB, a specificity-enhancing factor for the ClpXP proteolytic machine.
  Mol Cell, 12, 75-86.
PDB codes: 1ox8 1ox9
12663926 H.Zhang, Z.Yang, Y.Shen, and L.Tong (2003).
Crystal structure of the carboxyltransferase domain of acetyl-coenzyme A carboxylase.
  Science, 299, 2064-2067.
PDB codes: 1od2 1od4
12941278 J.A.Kenniston, T.A.Baker, J.M.Fernandez, and R.T.Sauer (2003).
Linkage between ATP consumption and mechanical unfolding during the protein processing reactions of an AAA+ degradation machine.
  Cell, 114, 511-520.  
12667450 J.M.Flynn, S.B.Neher, Y.I.Kim, R.T.Sauer, and T.A.Baker (2003).
Proteomic discovery of cellular substrates of the ClpXP protease reveals five classes of ClpX-recognition signals.
  Mol Cell, 11, 671-683.  
14635129 J.M.Petock, I.Y.Torshin, I.T.Weber, and R.W.Harrison (2003).
Analysis of protein structures reveals regions of rare backbone conformation at functional sites.
  Proteins, 53, 872-879.  
12424242 K.R.Marshall-Batty, and H.Nakai (2003).
Trans-targeting of the phage Mu repressor is promoted by conformational changes that expose its ClpX recognition determinant.
  J Biol Chem, 278, 1612-1617.  
12810958 M.Lucchiari-Hartz, V.Lindo, N.Hitziger, S.Gaedicke, L.Saveanu, P.M.van Endert, F.Greer, K.Eichmann, and G.Niedermann (2003).
Differential proteasomal processing of hydrophobic and hydrophilic protein regions: contribution to cytotoxic T lymphocyte epitope clustering in HIV-1-Nef.
  Proc Natl Acad Sci U S A, 100, 7755-7760.  
12805205 M.S.Kang, S.R.Kim, P.Kwack, B.K.Lim, S.W.Ahn, Y.M.Rho, I.S.Seong, S.C.Park, S.H.Eom, G.W.Cheong, and C.H.Chung (2003).
Molecular architecture of the ATP-dependent CodWX protease having an N-terminal serine active site.
  EMBO J, 22, 2893-2902.  
12717012 R.E.Burton, T.A.Baker, and R.T.Sauer (2003).
Energy-dependent degradation: Linkage between ClpX-catalyzed nucleotide hydrolysis and protein-substrate processing.
  Protein Sci, 12, 893-902.  
12950913 R.Hengge, and B.Bukau (2003).
Proteolysis in prokaryotes: protein quality control and regulatory principles.
  Mol Microbiol, 49, 1451-1462.  
14595014 S.B.Neher, R.T.Sauer, and T.A.Baker (2003).
Distinct peptide signals in the UmuD and UmuD' subunits of UmuD/D' mediate tethering and substrate processing by the ClpXP protease.
  Proc Natl Acad Sci U S A, 100, 13219-13224.  
14570582 S.Gottesman (2003).
Proteolysis in bacterial regulatory circuits.
  Annu Rev Cell Dev Biol, 19, 565-587.  
12675803 T.Tomoyasu, A.Takaya, E.Isogai, and T.Yamamoto (2003).
Turnover of FlhD and FlhC, master regulator proteins for Salmonella flagellum biogenesis, by the ATP-dependent ClpXP protease.
  Mol Microbiol, 48, 443-452.  
12937164 U.A.Wojtyra, G.Thibault, A.Tuite, and W.A.Houry (2003).
The N-terminal zinc binding domain of ClpX is a dimerization domain that modulates the chaperone function.
  J Biol Chem, 278, 48981-48990.  
11972783 B.Fischer, G.Rummel, P.Aldridge, and U.Jenal (2002).
The FtsH protease is involved in development, stress response and heat shock control in Caulobacter crescentus.
  Mol Microbiol, 44, 461-478.  
11982939 B.Zheng, T.Halperin, O.Hruskova-Heidingsfeldova, Z.Adam, and A.K.Clarke (2002).
Characterization of Chloroplast Clp proteins in Arabidopsis: Localization, tissue specificity and stress responses.
  Physiol Plant, 114, 92.  
11931773 D.A.Dougan, B.G.Reid, A.L.Horwich, and B.Bukau (2002).
ClpS, a substrate modulator of the ClpAP machine.
  Mol Cell, 9, 673-683.  
12445774 D.A.Wah, I.Levchenko, T.A.Baker, and R.T.Sauer (2002).
Characterization of a specificity factor for an AAA+ ATPase: assembly of SspB dimers with ssrA-tagged proteins and the ClpX hexamer.
  Chem Biol, 9, 1237-1245.  
12235156 F.Guo, L.Esser, S.K.Singh, M.R.Maurizi, and D.Xia (2002).
Crystal structure of the heterodimeric complex of the adaptor, ClpS, with the N-domain of the AAA+ chaperone, ClpA.
  J Biol Chem, 277, 46753-46762.
PDB codes: 1mbu 1mbv 1mbx
12205096 F.Guo, M.R.Maurizi, L.Esser, and D.Xia (2002).
Crystal structure of ClpA, an Hsp100 chaperone and regulator of ClpAP protease.
  J Biol Chem, 277, 46743-46752.
PDB codes: 1k6k 1ksf
12011053 I.S.Seong, M.S.Kang, M.K.Choi, J.W.Lee, O.J.Koh, J.Wang, S.H.Eom, and C.H.Chung (2002).
The C-terminal tails of HslU ATPase act as a molecular switch for activation of HslV peptidase.
  J Biol Chem, 277, 25976-25982.  
12234933 J.Ortega, H.S.Lee, M.R.Maurizi, and A.C.Steven (2002).
Alternating translocation of protein substrates from both ends of ClpXP protease.
  EMBO J, 21, 4938-4949.  
12177439 J.R.Hoskins, K.Yanagihara, K.Mizuuchi, and S.Wickner (2002).
ClpAP and ClpXP degrade proteins with tags located in the interior of the primary sequence.
  Proc Natl Acad Sci U S A, 99, 11037-11042.  
11994147 J.Viala, and P.Mazodier (2002).
ClpP-dependent degradation of PopR allows tightly regulated expression of the clpP3 clpP4 operon in Streptomyces lividans.
  Mol Microbiol, 44, 633-643.  
12077445 K.Zeth, D.A.Dougan, S.Cusack, B.Bukau, and R.B.Ravelli (2002).
Crystallization and preliminary X-ray analysis of the Escherichia coli adaptor protein ClpS, free and in complex with the N-terminal domain of ClpA.
  Acta Crystallogr D Biol Crystallogr, 58, 1207-1210.  
12426582 K.Zeth, R.B.Ravelli, K.Paal, S.Cusack, B.Bukau, and D.A.Dougan (2002).
Structural analysis of the adaptor protein ClpS in complex with the N-terminal domain of ClpA.
  Nat Struct Biol, 9, 906-911.
PDB codes: 1lzw 1mg9
12208995 R.Hengge-Aronis (2002).
Signal transduction and regulatory mechanisms involved in control of the sigma(S) (RpoS) subunit of RNA polymerase.
  Microbiol Mol Biol Rev, 66, 373.  
12032294 R.Ramachandran, C.Hartmann, H.K.Song, R.Huber, and M.Bochtler (2002).
Functional interactions of HslV (ClpQ) with the ATPase HslU (ClpY).
  Proc Natl Acad Sci U S A, 99, 7396-7401.  
12169602 S.Chiba, Y.Akiyama, and K.Ito (2002).
Membrane protein degradation by FtsH can be initiated from either end.
  J Bacteriol, 184, 4775-4782.  
12270812 S.Fedhila, T.Msadek, P.Nel, and D.Lereclus (2002).
Distinct clpP genes control specific adaptive responses in Bacillus thuringiensis.
  J Bacteriol, 184, 5554-5562.  
11923310 S.G.Kang, J.Ortega, S.K.Singh, N.Wang, N.N.Huang, A.C.Steven, and M.R.Maurizi (2002).
Functional proteolytic complexes of the human mitochondrial ATP-dependent protease, hClpXP.
  J Biol Chem, 277, 21095-21102.  
12057965 T.Fukui, T.Eguchi, H.Atomi, and T.Imanaka (2002).
A membrane-bound archaeal Lon protease displays ATP-independent proteolytic activity towards unfolded proteins and ATP-dependent activity for folded proteins.
  J Bacteriol, 184, 3689-3698.  
11919638 T.Krojer, M.Garrido-Franco, R.Huber, M.Ehrmann, and T.Clausen (2002).
Crystal structure of DegP (HtrA) reveals a new protease-chaperone machine.
  Nature, 416, 455-459.
PDB code: 1ky9
11807061 T.Pummi, S.Leskelä, E.Wahlström, U.Gerth, H.Tjalsma, M.Hecker, M.Sarvas, and V.P.Kontinen (2002).
ClpXP protease regulates the signal peptide cleavage of secretory preproteins in Bacillus subtilis with a mechanism distinct from that of the Ecs ABC transporter.
  J Bacteriol, 184, 1010-1018.  
12399180 Z.Adam, and A.K.Clarke (2002).
Cutting edge of chloroplast proteolysis.
  Trends Plant Sci, 7, 451-456.  
11259663 B.G.Reid, W.A.Fenton, A.L.Horwich, and E.U.Weber-Ban (2001).
ClpA mediates directional translocation of substrate proteins into the ClpP protease.
  Proc Natl Acad Sci U S A, 98, 3768-3772.  
11463387 C.Lee, M.P.Schwartz, S.Prakash, M.Iwakura, and A.Matouschek (2001).
ATP-dependent proteases degrade their substrates by processively unraveling them from the degradation signal.
  Mol Cell, 7, 627-637.  
11454203 D.Frees, P.Varmanen, and H.Ingmer (2001).
Inactivation of a gene that is highly conserved in Gram-positive bacteria stimulates degradation of non-native proteins and concomitantly increases stress tolerance in Lactococcus lactis.
  Mol Microbiol, 41, 93.  
11454184 D.P.Bogdanos, K.Choudhuri, and D.Vergani (2001).
Molecular mimicry and autoimmune liver disease: virtuous intentions, malign consequences.
  Liver, 21, 225-232.  
11395407 J.A.Gerlt, and P.C.Babbitt (2001).
Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies.
  Annu Rev Biochem, 70, 209-246.  
11344323 J.H.Lo, T.A.Baker, and R.T.Sauer (2001).
Characterization of the N-terminal repeat domain of Escherichia coli ClpA-A class I Clp/HSP100 ATPase.
  Protein Sci, 10, 551-559.  
11535833 J.M.Flynn, I.Levchenko, M.Seidel, S.H.Wickner, R.T.Sauer, and T.A.Baker (2001).
Overlapping recognition determinants within the ssrA degradation tag allow modulation of proteolysis.
  Proc Natl Acad Sci U S A, 98, 10584-10589.  
11709174 J.Wang, J.J.Song, I.S.Seong, M.C.Franklin, S.Kamtekar, S.H.Eom, and C.H.Chung (2001).
Nucleotide-dependent conformational changes in a protease-associated ATPase HsIU.
  Structure, 9, 1107-1116.
PDB codes: 1hqy 1ht1 1ht2
11250202 J.Wang, J.J.Song, M.C.Franklin, S.Kamtekar, Y.J.Im, S.H.Rho, I.S.Seong, C.S.Lee, C.H.Chung, and S.H.Eom (2001).
Crystal structures of the HslVU peptidase-ATPase complex reveal an ATP-dependent proteolysis mechanism.
  Structure, 9, 177-184.
PDB codes: 1g4a 1g4b
11544370 M.Mock, and A.Fouet (2001).
  Annu Rev Microbiol, 55, 647-671.  
11406586 R.E.Burton, S.M.Siddiqui, Y.I.Kim, T.A.Baker, and R.T.Sauer (2001).
Effects of protein stability and structure on substrate processing by the ClpXP unfolding and degradation machine.
  EMBO J, 20, 3092-3100.  
11287666 T.Ishikawa, F.Beuron, M.Kessel, S.Wickner, M.R.Maurizi, and A.C.Steven (2001).
Translocation pathway of protein substrates in ClpAP protease.
  Proc Natl Acad Sci U S A, 98, 4328-4333.  
11473577 T.Ogura, and A.J.Wilkinson (2001).
AAA+ superfamily ATPases: common structure--diverse function.
  Genes Cells, 6, 575-597.  
11238382 Y.Zhou, S.Gottesman, J.R.Hoskins, M.R.Maurizi, and S.Wickner (2001).
The RssB response regulator directly targets sigma(S) for degradation by ClpXP.
  Genes Dev, 15, 627-637.  
11084366 C.M.Pickart (2000).
Ubiquitin in chains.
  Trends Biochem Sci, 25, 544-548.  
10809708 E.Krüger, E.Witt, S.Ohlmeier, R.Hanschke, and M.Hecker (2000).
The clp proteases of Bacillus subtilis are directly involved in degradation of misfolded proteins.
  J Bacteriol, 182, 3259-3265.  
10998626 G.Evans, P.Roversi, and G.Bricogne (2000).
In-house low-resolution X-ray crystallography.
  Acta Crystallogr D Biol Crystallogr, 56, 1304-1311.  
10692374 H.L.Wilson, M.S.Ou, H.C.Aldrich, and J.Maupin-Furlow (2000).
Biochemical and physical properties of the Methanococcus jannaschii 20S proteasome and PAN, a homolog of the ATPase (Rpt) subunits of the eucaryal 26S proteasome.
  J Bacteriol, 182, 1680-1692.  
  11178260 J.A.Gerlt, and P.C.Babbitt (2000).
Can sequence determine function?
  Genome Biol, 1, REVIEWS0005.  
11163224 J.Ortega, S.K.Singh, T.Ishikawa, M.R.Maurizi, and A.C.Steven (2000).
Visualization of substrate binding and translocation by the ATP-dependent protease, ClpXP.
  Mol Cell, 6, 1515-1521.  
10922051 J.R.Hoskins, S.K.Singh, M.R.Maurizi, and S.Wickner (2000).
Protein binding and unfolding by the chaperone ClpA and degradation by the protease ClpAP.
  Proc Natl Acad Sci U S A, 97, 8892-8897.  
11069683 J.Viala, G.Rapoport, and P.Mazodier (2000).
The clpP multigenic family in Streptomyces lividans: conditional expression of the clpP3 clpP4 operon is controlled by PopR, a novel transcriptional activator.
  Mol Microbiol, 38, 602-612.  
11106384 K.Håkansson, A.H.Wang, and C.G.Miller (2000).
The structure of aspartyl dipeptidase reveals a unique fold with a Ser-His-Glu catalytic triad.
  Proc Natl Acad Sci U S A, 97, 14097-14102.
PDB codes: 1fy2 1fye
10745003 M.E.Gottesman, and W.A.Hendrickson (2000).
Protein folding and unfolding by Escherichia coli chaperones and chaperonins.
  Curr Opin Microbiol, 3, 197-202.  
  11005383 M.J.Eriksson, and A.K.Clarke (2000).
The Escherichia coli heat shock protein ClpB restores acquired thermotolerance to a cyanobacterial clpB deletion mutant.
  Cell Stress Chaperones, 5, 255-264.  
10760131 O.Gaillot, E.Pellegrini, S.Bregenholt, S.Nair, and P.Berche (2000).
The ClpP serine protease is essential for the intracellular parasitism and virulence of Listeria monocytogenes.
  Mol Microbiol, 35, 1286-1294.  
10922052 S.K.Singh, R.Grimaud, J.R.Hoskins, S.Wickner, and M.R.Maurizi (2000).
Unfolding and internalization of proteins by the ATP-dependent proteases ClpXP and ClpAP.
  Proc Natl Acad Sci U S A, 97, 8898-8903.  
11114201 X.Du, I.G.Choi, R.Kim, W.Wang, J.Jancarik, H.Yokota, and S.H.Kim (2000).
Crystal structure of an intracellular protease from Pyrococcus horikoshii at 2-A resolution.
  Proc Natl Acad Sci U S A, 97, 14079-14084.
PDB code: 1g2i
10882100 Y.I.Kim, R.E.Burton, B.M.Burton, R.T.Sauer, and T.A.Baker (2000).
Dynamics of substrate denaturation and translocation by the ClpXP degradation machine.
  Mol Cell, 5, 639-648.  
10455123 A.Bolhuis, A.Matzen, H.L.Hyyryläinen, V.P.Kontinen, R.Meima, J.Chapuis, G.Venema, S.Bron, R.Freudl, and J.M.van Dijl (1999).
Signal peptide peptidase- and ClpP-like proteins of Bacillus subtilis required for efficient translocation and processing of secretory proteins.
  J Biol Chem, 274, 24585-24592.  
10500119 A.L.Horwich, E.U.Weber-Ban, and D.Finley (1999).
Chaperone rings in protein folding and degradation.
  Proc Natl Acad Sci U S A, 96, 11033-11040.  
10359771 C.K.Smith, T.A.Baker, and R.T.Sauer (1999).
Lon and Clp family proteases and chaperones share homologous substrate-recognition domains.
  Proc Natl Acad Sci U S A, 96, 6678-6682.  
9987112 D.Frees, and H.Ingmer (1999).
ClpP participates in the degradation of misfolded protein in Lactococcus lactis.
  Mol Microbiol, 31, 79-87.  
10872471 D.Voges, P.Zwickl, and W.Baumeister (1999).
The 26S proteasome: a molecular machine designed for controlled proteolysis.
  Annu Rev Biochem, 68, 1015-1068.  
10358024 E.Gazit, and R.T.Sauer (1999).
The Doc toxin and Phd antidote proteins of the bacteriophage P1 plasmid addiction system form a heterotrimeric complex.
  J Biol Chem, 274, 16813-16818.  
  10482525 H.L.Wilson, H.C.Aldrich, and J.Maupin-Furlow (1999).
Halophilic 20S proteasomes of the archaeon Haloferax volcanii: purification, characterization, and gene sequence analysis.
  J Bacteriol, 181, 5814-5824.  
10359790 H.Stahlberg, E.Kutejová, K.Suda, B.Wolpensinger, A.Lustig, G.Schatz, A.Engel, and C.K.Suzuki (1999).
Mitochondrial Lon of Saccharomyces cerevisiae is a ring-shaped protease with seven flexible subunits.
  Proc Natl Acad Sci U S A, 96, 6787-6790.  
10387003 H.Xiang, L.Luo, K.L.Taylor, and D.Dunaway-Mariano (1999).
Interchange of catalytic activity within the 2-enoyl-coenzyme A hydratase/isomerase superfamily based on a common active site template.
  Biochemistry, 38, 7638-7652.  
10320569 J.Porankiewicz, J.Wang, and A.K.Clarke (1999).
New insights into the ATP-dependent Clp protease: Escherichia coli and beyond.
  Mol Microbiol, 32, 449-458.  
10339542 L.Van Melderen, and S.Gottesman (1999).
Substrate sequestration by a proteolytically inactive Lon mutant.
  Proc Natl Acad Sci U S A, 96, 6064-6071.  
10318812 M.Gonciarz-Swiatek, A.Wawrzynow, S.J.Um, B.A.Learn, R.McMacken, W.L.Kelley, C.Georgopoulos, O.Sliekers, and M.Zylicz (1999).
Recognition, targeting, and hydrolysis of the lambda O replication protein by the ClpP/ClpX protease.
  J Biol Chem, 274, 13999-14005.  
  10322004 M.Osterås, A.Stotz, S.Schmid Nuoffer, and U.Jenal (1999).
Identification and transcriptional control of the genes encoding the Caulobacter crescentus ClpXP protease.
  J Bacteriol, 181, 3039-3050.  
10383442 M.Pak, J.R.Hoskins, S.K.Singh, M.R.Maurizi, and S.Wickner (1999).
Concurrent chaperone and protease activities of ClpAP and the requirement for the N-terminal ClpA ATP binding site for chaperone activity.
  J Biol Chem, 274, 19316-19322.  
10508673 M.Schmidt, A.N.Lupas, and D.Finley (1999).
Structure and mechanism of ATP-dependent proteases.
  Curr Opin Chem Biol, 3, 584-591.  
10231573 N.Knipfer, A.Seth, S.G.Roudiak, and T.E.Shrader (1999).
Species variation in ATP-dependent protein degradation: protease profiles differ between mycobacteria and protease functions differ between Mycobacterium smegmatis and Escherichia coli.
  Gene, 231, 95.  
10081087 R.De Mot, I.Nagy, J.Walz, and W.Baumeister (1999).
Proteasomes and other self-compartmentalizing proteases in prokaryotes.
  Trends Microbiol, 7, 88-92.  
10322171 S.Gottesman (1999).
Regulation by proteolysis: developmental switches.
  Curr Opin Microbiol, 2, 142-147.  
10555973 S.K.Singh, F.Guo, and M.R.Maurizi (1999).
ClpA and ClpP remain associated during multiple rounds of ATP-dependent protein degradation by ClpAP protease.
  Biochemistry, 38, 14906-14915.  
10347188 S.Santagata, D.Bhattacharyya, F.H.Wang, N.Singha, A.Hodtsev, and E.Spanopoulou (1999).
Molecular cloning and characterization of a mouse homolog of bacterial ClpX, a novel mammalian class II member of the Hsp100/Clp chaperone family.
  J Biol Chem, 274, 16311-16319.  
10583944 S.Wickner, M.R.Maurizi, and S.Gottesman (1999).
Posttranslational quality control: folding, refolding, and degrading proteins.
  Science, 286, 1888-1893.  
10411867 S.Wickner, and M.R.Maurizi (1999).
Here's the hook: similar substrate binding sites in the chaperone domains of Clp and Lon.
  Proc Natl Acad Sci U S A, 96, 8318-8320.  
10320574 Crécy-Lagard, P.Servant-Moisson, J.Viala, C.Grandvalet, and P.Mazodier (1999).
Alteration of the synthesis of the Clp ATP-dependent protease affects morphological and physiological differentiation in Streptomyces.
  Mol Microbiol, 32, 505-517.  
9666335 A.G.Murzin (1998).
How far divergent evolution goes in proteins.
  Curr Opin Struct Biol, 8, 380-387.  
9651675 H.P.Feng, and L.M.Gierasch (1998).
Molecular chaperones: clamps for the Clps?
  Curr Biol, 8, R464-R467.  
9770452 J.R.Hoskins, M.Pak, M.R.Maurizi, and S.Wickner (1998).
The role of the ClpA chaperone in proteolysis by ClpAP.
  Proc Natl Acad Sci U S A, 95, 12135-12140.  
9890793 K.Turgay, J.Hahn, J.Burghoorn, and D.Dubnau (1998).
Competence in Bacillus subtilis is controlled by regulated proteolysis of a transcription factor.
  EMBO J, 17, 6730-6738.  
9601038 M.R.Maurizi, S.K.Singh, M.W.Thompson, M.Kessel, and A.Ginsburg (1998).
Molecular properties of ClpAP protease of Escherichia coli: ATP-dependent association of ClpA and clpP.
  Biochemistry, 37, 7778-7786.  
9845366 N.Tamura, F.Lottspeich, W.Baumeister, and T.Tamura (1998).
The role of tricorn protease and its aminopeptidase-interacting factors in cellular protein degradation.
  Cell, 95, 637-648.  
9575205 R.Grimaud, M.Kessel, F.Beuron, A.C.Steven, and M.R.Maurizi (1998).
Enzymatic and structural similarities between the Escherichia coli ATP-dependent proteases, ClpXP and ClpAP.
  J Biol Chem, 273, 12476-12481.  
9698372 S.G.Roudiak, and T.E.Shrader (1998).
Functional role of the N-terminal region of the Lon protease from Mycobacterium smegmatis.
  Biochemistry, 37, 11255-11263.  
  9573050 S.Gottesman, E.Roche, Y.Zhou, and R.T.Sauer (1998).
The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system.
  Genes Dev, 12, 1338-1347.  
9722513 S.J.Yoo, H.H.Kim, D.H.Shin, C.S.Lee, I.S.Seong, J.H.Seol, N.Shimbara, K.Tanaka, and C.H.Chung (1998).
Effects of the cys mutations on structure and function of the ATP-dependent HslVU protease in Escherichia coli. The Cys287 to Val mutation in HslU uncouples the ATP-dependent proteolysis by HslvU from ATP hydrolysis.
  J Biol Chem, 273, 22929-22935.  
9643546 U.Gerth, E.Krüger, I.Derré, T.Msadek, and M.Hecker (1998).
Stress induction of the Bacillus subtilis clpP gene encoding a homologue of the proteolytic component of the Clp protease and the involvement of ClpP and ClpX in stress tolerance.
  Mol Microbiol, 28, 787-802.  
9755166 U.Jenal, and T.Fuchs (1998).
An essential protease involved in bacterial cell-cycle control.
  EMBO J, 17, 5658-5669.  
9476896 W.Baumeister, J.Walz, F.Zühl, and E.Seemüller (1998).
The proteasome: paradigm of a self-compartmentalizing protease.
  Cell, 92, 367-380.  
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