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PDBsum entry 1tyf

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protein Protein-protein interface(s) links
Peptidase PDB id
1tyf
Jmol
Contents
Protein chains
(+ 8 more) 183 a.a. *
Waters ×1246
* Residue conservation analysis
PDB id:
1tyf
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)
Resolution:
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
Date:
13-Oct-97     Release date:   17-Jun-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 Enzyme reactions 
   Enzyme class: E.C.3.4.21.92  - 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.
 
  ABSTRACT  
 
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.
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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.
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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.
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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).
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15205439 J.Liu, and A.Mushegian (2004).
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15064753 S.A.Joshi, G.L.Hersch, T.A.Baker, and R.T.Sauer (2004).
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14679237 U.Gerth, J.Kirstein, J.Mostertz, T.Waldminghaus, M.Miethke, H.Kock, and M.Hecker (2004).
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PDB code: 1l1j
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PDB code: 1um8
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PDB codes: 1ox8 1ox9
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12941278 J.A.Kenniston, T.A.Baker, J.M.Fernandez, and R.T.Sauer (2003).
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14635129 J.M.Petock, I.Y.Torshin, I.T.Weber, and R.W.Harrison (2003).
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12675803 T.Tomoyasu, A.Takaya, E.Isogai, and T.Yamamoto (2003).
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PDB codes: 1k6k 1ksf
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