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PDBsum entry 1doo

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protein ligands Protein-protein interface(s) links
Chaperone PDB id
1doo
Jmol
Contents
Protein chains
173 a.a.
393 a.a.
Ligands
ANP ×2
Superseded by: 1e94
PDB id:
1doo
Name: Chaperone
Title: Heat shock locus v (hslv)-heat shock locus u (hslu) from e. Coli
Structure: Heat shock locus v. Chain: a, b, c, d. Synonym: hslv. Engineered: yes. Heat shock locus u. Chain: e, f. Synonym: hslu. Engineered: yes
Source: Escherichia coli. Bacteria. Strain: xl-1 blue. Cellular_location: cytoplasm. Expressed in: escherichia coli.
Biol. unit: Hexamer (from PDB file)
Resolution:
2.81Å     R-factor:   0.301     R-free:   0.349
Authors: M.Bochtler,C.Hartmann,H.K.Song,G.P.Bourenkov,H.D.Bartunik
Key ref:
M.Bochtler et al. (2000). The structures of HsIU and the ATP-dependent protease HsIU-HsIV. Nature, 403, 800-805. PubMed id: 10693812 DOI: 10.1038/35001629
Date:
21-Dec-99     Release date:   18-Feb-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam  
P31059  (HSLV_ECOLI) - 
Protein chains
Pfam  
P32168  (HSLU_ECOLI) - 
Key:    Secondary structure

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: E.C.3.4.99.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1038/35001629 Nature 403:800-805 (2000)
PubMed id: 10693812  
 
 
The structures of HsIU and the ATP-dependent protease HsIU-HsIV.
M.Bochtler, C.Hartmann, H.K.Song, G.P.Bourenkov, H.D.Bartunik, R.Huber.
 
  ABSTRACT  
 
The degradation of cytoplasmic proteins is an ATP-dependent process. Substrates are targeted to a single soluble protease, the 26S proteasome, in eukaryotes and to a number of unrelated proteases in prokaryotes. A surprising link emerged with the discovery of the ATP-dependent protease HslVU (heat shock locus VU) in Escherichia coli. Its protease component HslV shares approximately 20% sequence similarity and a conserved fold with 20S proteasome beta-subunits. HslU is a member of the Hsp100 (Clp) family of ATPases. Here we report the crystal structures of free HslU and an 820,000 relative molecular mass complex of HslU and HslV-the first structure of a complete set of components of an ATP-dependent protease. HslV and HslU display sixfold symmetry, ruling out mechanisms of protease activation that require a symmetry mismatch between the two components. Instead, there is conformational flexibility and domain motion in HslU and a localized order-disorder transition in HslV. Individual subunits of HslU contain two globular domains in relative orientations that correlate with nucleotide bound and unbound states. They are surprisingly similar to their counterparts in N-ethylmaleimide-sensitive fusion protein, the prototype of an AAA-ATPase. A third, mostly alpha-helical domain in HslU mediates the contact with HslV and may be the structural equivalent of the amino-terminal domains in proteasomal AAA-ATPases.
 
  Selected figure(s)  
 
Figure 1.
Figure 1: Summary of the three crystal forms (a-c) that were used for structure determination. Subunits in the respective asymmetric units are numbered 1-6.
Figure 2.
Figure 2: Comparison of HsIU and NSF main chains. a, Superposition of the ligand-bound (coloured) and free (white) HslU forms. Chains 1 and 2 of the P321 crystals (see Fig. 1c) are shown. The N domains (shown in green and red) have been superimposed (r.m.s.d. C bond lengths = 0.5 for the central -sheet, r.m.s.d. C bond lengths = 1.2 for the whole domain). For clarity, the N and I domains of the free form have been omitted. b, Stereo diagram of NSF D2.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nature (2000, 403, 800-805) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
23023677 R.M.Raju, A.L.Goldberg, and E.J.Rubin (2012).
Bacterial proteolytic complexes as therapeutic targets.
  Nat Rev Drug Discov, 11, 777-789.  
22562135 S.E.Glynn, A.R.Nager, T.A.Baker, and R.T.Sauer (2012).
Dynamic and static components power unfolding in topologically closed rings of a AAA+ proteolytic machine.
  Nat Struct Mol Biol, 19, 616-622.  
21266546 A.Kravats, M.Jayasinghe, and G.Stan (2011).
Unfolding and translocation pathway of substrate protein controlled by structure in repetitive allosteric cycles of the ClpY ATPase.
  Proc Natl Acad Sci U S A, 108, 2234-2239.  
21330489 A.P.Carter, C.Cho, L.Jin, and R.D.Vale (2011).
Crystal structure of the dynein motor domain.
  Science, 331, 1159-1165.
PDB code: 3qmz
21335235 D.M.Smith, H.Fraga, C.Reis, G.Kafri, and A.L.Goldberg (2011).
ATP binds to proteasomal ATPases in pairs with distinct functional effects, implying an ordered reaction cycle.
  Cell, 144, 526-538.  
22037170 G.Tian, S.Park, M.J.Lee, B.Huck, F.McAllister, C.P.Hill, S.P.Gygi, and D.Finley (2011).
An asymmetric interface between the regulatory and core particles of the proteasome.
  Nat Struct Mol Biol, 18, 1259-1267.  
20305655 B.G.Lee, E.Y.Park, K.E.Lee, H.Jeon, K.H.Sung, H.Paulsen, H.Rübsamen-Schaeff, H.Brötz-Oesterhelt, and H.K.Song (2010).
Structures of ClpP in complex with acyldepsipeptide antibiotics reveal its activation mechanism.
  Nat Struct Mol Biol, 17, 471-478.
PDB codes: 3ktg 3kth 3kti 3ktj 3ktk
20462489 G.Effantin, T.Ishikawa, G.M.De Donatis, M.R.Maurizi, and A.C.Steven (2010).
Local and global mobility in the ClpA AAA+ chaperone detected by cryo-electron microscopy: functional connotations.
  Structure, 18, 553-562.  
21148420 M.El Bakkouri, I.Gutsche, U.Kanjee, B.Zhao, M.Yu, G.Goret, G.Schoehn, W.P.Burmeister, and W.A.Houry (2010).
Structure of RavA MoxR AAA+ protein reveals the design principles of a molecular cage modulating the inducible lysine decarboxylase activity.
  Proc Natl Acad Sci U S A, 107, 22499-22504.
PDB code: 3nbx
20541423 N.Gallastegui, and M.Groll (2010).
The 26S proteasome: assembly and function of a destructive machine.
  Trends Biochem Sci, 35, 634-642.  
19955424 C.Bieniossek, B.Niederhauser, and U.M.Baumann (2009).
The crystal structure of apo-FtsH reveals domain movements necessary for substrate unfolding and translocation.
  Proc Natl Acad Sci U S A, 106, 21579-21584.
PDB code: 3kds
19489727 D.Finley (2009).
Recognition and processing of ubiquitin-protein conjugates by the proteasome.
  Annu Rev Biochem, 78, 477-513.  
19374766 D.Gangwar, M.K.Kalita, D.Gupta, V.S.Chauhan, and A.Mohmmed (2009).
A systematic classification of Plasmodium falciparum P-loop NTPases: structural and functional correlation.
  Malar J, 8, 69.  
19362814 F.Striebel, W.Kress, and E.Weber-Ban (2009).
Controlled destruction: AAA+ ATPases in protein degradation from bacteria to eukaryotes.
  Curr Opin Struct Biol, 19, 209-217.  
19395483 H.Y.Lien, R.S.Shy, S.S.Peng, Y.L.Wu, Y.T.Weng, H.H.Chen, P.C.Su, W.F.Ng, Y.C.Chen, P.Y.Chang, and W.F.Wu (2009).
Characterization of the Escherichia coli ClpY (HslU) substrate recognition site in the ClpYQ (HslUV) protease using the yeast two-hybrid system.
  J Bacteriol, 191, 4218-4231.  
19801685 J.W.Lee, E.Park, M.S.Jeong, Y.J.Jeon, S.H.Eom, J.H.Seol, and C.H.Chung (2009).
HslVU ATP-dependent protease utilizes maximally six among twelve threonine active sites during proteolysis.
  J Biol Chem, 284, 33475-33484.  
19836328 N.Gallastegui, and M.Groll (2009).
How ATPases unravel a mystery.
  Structure, 17, 1279-1281.  
19828442 N.Koga, T.Kameda, K.Okazaki, and S.Takada (2009).
Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations.
  Proc Natl Acad Sci U S A, 106, 18237-18242.  
19363223 N.Medalia, A.Beer, P.Zwickl, O.Mihalache, M.Beck, O.Medalia, and A.Navon (2009).
Architecture and molecular mechanism of PAN, the archaeal proteasome regulatory ATPase.
  J Biol Chem, 284, 22952-22960.  
19362537 P.Wendler, J.Shorter, D.Snead, C.Plisson, D.K.Clare, S.Lindquist, and H.R.Saibil (2009).
Motor mechanism for protein threading through Hsp104.
  Mol Cell, 34, 81-92.  
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
19690374 S.Hare, P.Cherepanov, and J.Wang (2009).
Application of general formulas for the correction of a lattice-translocation defect in crystals of a lentiviral integrase in complex with LEDGF.
  Acta Crystallogr D Biol Crystallogr, 65, 966-973.  
19008106 S.M.Doyle, and S.Wickner (2009).
Hsp104 and ClpB: protein disaggregating machines.
  Trends Biochem Sci, 34, 40-48.  
19452133 W.Hwang, and M.J.Lang (2009).
Mechanical design of translocating motor proteins.
  Cell Biochem Biophys, 54, 11-22.  
18974091 A.Luthra, A.Mahmood, A.Arora, and R.Ramachandran (2008).
Characterization of Rv3868, an essential hypothetical protein of the ESX-1 secretion system in Mycobacterium tuberculosis.
  J Biol Chem, 283, 36532-36541.  
18931677 A.Martin, T.A.Baker, and R.T.Sauer (2008).
Pore loops of the AAA+ ClpX machine grip substrates to drive translocation and unfolding.
  Nat Struct Mol Biol, 15, 1147-1151.  
18313382 A.Martin, T.A.Baker, and R.T.Sauer (2008).
Diverse pore loops of the AAA+ ClpX machine mediate unassisted and adaptor-dependent recognition of ssrA-tagged substrates.
  Mol Cell, 29, 441-450.  
18703850 B.Stec, and K.A.Stieglitz (2008).
Not so clear on oxygen. Comment on Structural basis for cofactor-independent dioxygenation in vancomycin biosynthesis by Widboom et al. (2007), Nature (London), 447, 342-345.
  Acta Crystallogr D Biol Crystallogr, 64, 1000-1002.  
18838376 E.Park, J.W.Lee, S.H.Eom, J.H.Seol, and C.H.Chung (2008).
Binding of MG132 or Deletion of the Thr Active Sites in HslV Subunits Increases the Affinity of HslV Protease for HslU ATPase and Makes This Interaction Nucleotide-independent.
  J Biol Chem, 283, 33258-33266.  
18421150 E.Y.Park, and H.K.Song (2008).
A degradation signal recognition in prokaryotes.
  J Synchrotron Radiat, 15, 246-249.  
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.  
18689473 L.A.Simmons, A.D.Grossman, and G.C.Walker (2008).
Clp and Lon proteases occupy distinct subcellular positions in Bacillus subtilis.
  J Bacteriol, 190, 6758-6768.  
18332143 L.C.Briggs, G.S.Baldwin, N.Miyata, H.Kondo, X.Zhang, and P.S.Freemont (2008).
Analysis of nucleotide binding to P97 reveals the properties of a tandem AAA hexameric ATPase.
  J Biol Chem, 283, 13745-13752.  
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.  
18550799 L.Zhu, J.O.Wrabl, A.P.Hayashi, L.S.Rose, and P.J.Thomas (2008).
The torsin-family AAA+ protein OOC-5 contains a critical disulfide adjacent to Sensor-II that couples redox state to nucleotide binding.
  Mol Biol Cell, 19, 3599-3612.  
18647240 N.D.Thomsen, and J.M.Berger (2008).
Structural frameworks for considering microbial protein- and nucleic acid-dependent motor ATPases.
  Mol Microbiol, 69, 1071-1090.  
18755692 R.Lum, M.Niggemann, and J.R.Glover (2008).
Peptide and Protein Binding in the Axial Channel of Hsp104: INSIGHTS INTO THE MECHANISM OF PROTEIN UNFOLDING.
  J Biol Chem, 283, 30139-30150.  
18849995 X.Zhang, and D.B.Wigley (2008).
The 'glutamate switch' provides a link between ATPase activity and ligand binding in AAA+ proteins.
  Nat Struct Mol Biol, 15, 1223-1227.  
18421378 Z.Li, M.E.Lindsay, S.A.Motyka, P.T.Englund, and C.C.Wang (2008).
Identification of a bacterial-like HslVU protease in the mitochondria of Trypanosoma brucei and its role in mitochondrial DNA replication.
  PLoS Pathog, 4, e1000048.  
18280501 Z.Yu, M.D.Gonciarz, W.I.Sundquist, C.P.Hill, and G.J.Jensen (2008).
Cryo-EM structure of dodecameric Vps4p and its 2:1 complex with Vta1p.
  J Mol Biol, 377, 364-377.  
17553803 A.A.Horwitz, A.Navon, M.Groll, D.M.Smith, C.Reis, and A.L.Goldberg (2007).
ATP-induced structural transitions in PAN, the proteasome-regulatory ATPase complex in Archaea.
  J Biol Chem, 282, 22921-22929.  
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.  
18078545 C.D.Putnam, M.Hammel, G.L.Hura, and J.A.Tainer (2007).
X-ray solution scattering (SAXS) combined with crystallography and computation: defining accurate macromolecular structures, conformations and assemblies in solution.
  Q Rev Biophys, 40, 191-285.  
17803938 D.M.Smith, S.C.Chang, S.Park, D.Finley, Y.Cheng, and A.L.Goldberg (2007).
Docking of the proteasomal ATPases' carboxyl termini in the 20S proteasome's alpha ring opens the gate for substrate entry.
  Mol Cell, 27, 731-744.  
17393462 I.Aksentijevich, C.D Putnam, E.F.Remmers, J.L.Mueller, J.Le, R.D.Kolodner, Z.Moak, M.Chuang, F.Austin, R.Goldbach-Mansky, H.M.Hoffman, and D.L.Kastner (2007).
The clinical continuum of cryopyrinopathies: novel CIAS1 mutations in North American patients and a new cryopyrin model.
  Arthritis Rheum, 56, 1273-1285.  
17915007 J.Larsen, P.Kuhnert, J.Frey, H.Christensen, M.Bisgaard, and J.E.Olsen (2007).
Analysis of gene order data supports vertical inheritance of the leukotoxin operon and genome rearrangements in the 5' flanking region in genus Mannheimia.
  BMC Evol Biol, 7, 184.  
17202259 K.Imada, T.Minamino, A.Tahara, and K.Namba (2007).
Structural similarity between the flagellar type III ATPase FliI and F1-ATPase subunits.
  Proc Natl Acad Sci U S A, 104, 485-490.
PDB code: 2dpy
17522969 M.K.Azim, and S.Noor (2007).
Characterization of protomer interfaces in HslV protease; the bacterial homologue of 20S proteasome.
  Protein J, 26, 213-219.  
18160044 P.Wendler, J.Shorter, C.Plisson, A.G.Cashikar, S.Lindquist, and H.R.Saibil (2007).
Atypical AAA+ subunit packing creates an expanded cavity for disaggregation by the protein-remodeling factor Hsp104.
  Cell, 131, 1366-1377.  
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.  
16484367 C.Bieniossek, T.Schalch, M.Bumann, M.Meister, R.Meier, and U.Baumann (2006).
The molecular architecture of the metalloprotease FtsH.
  Proc Natl Acad Sci U S A, 103, 3066-3071.
PDB codes: 2ce7 2cea
16361263 F.I.Andersson, R.Blakytny, J.Kirstein, K.Turgay, B.Bukau, A.Mogk, and A.K.Clarke (2006).
Cyanobacterial ClpC/HSP100 protein displays intrinsic chaperone activity.
  J Biol Chem, 281, 5468-5475.  
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.  
16689629 J.P.Erzberger, and J.M.Berger (2006).
Evolutionary relationships and structural mechanisms of AAA+ proteins.
  Annu Rev Biophys Biomol Struct, 35, 93.  
17021930 M.X.Ruiz-González, and I.Marín (2006).
Proteasome-related HslU and HslV genes typical of eubacteria are widespread in eukaryotes.
  J Mol Evol, 63, 504-512.  
16973614 N.Joly, J.Schumacher, and M.Buck (2006).
Heterogeneous nucleotide occupancy stimulates functionality of phage shock protein F, an AAA+ transcriptional activator.
  J Biol Chem, 281, 34997-35007.  
17021621 P.C.Stirling, S.F.Bakhoum, A.B.Feigl, and M.R.Leroux (2006).
Convergent evolution of clamp-like binding sites in diverse chaperones.
  Nat Struct Mol Biol, 13, 865-870.  
16463102 R.J.Sawers, J.Viney, P.R.Farmer, R.R.Bussey, G.Olsefski, K.Anufrikova, C.N.Hunter, and T.P.Brutnell (2006).
The maize Oil yellow1 (Oy1) gene encodes the I subunit of magnesium chelatase.
  Plant Mol Biol, 60, 95.  
17074491 T.A.Baker, and R.T.Sauer (2006).
ATP-dependent proteases of bacteria: recognition logic and operating principles.
  Trends Biochem Sci, 31, 647-653.  
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.  
16237435 A.Martin, T.A.Baker, and R.T.Sauer (2005).
Rebuilt AAA + motors reveal operating principles for ATP-fuelled machines.
  Nature, 437, 1115-1120.  
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.  
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.  
15849200 E.Park, Y.M.Rho, O.J.Koh, S.W.Ahn, I.S.Seong, J.J.Song, O.Bang, J.H.Seol, J.Wang, S.H.Eom, and C.H.Chung (2005).
Role of the GYVG pore motif of HslU ATPase in protein unfolding and translocation for degradation by HslV peptidase.
  J Biol Chem, 280, 22892-22898.  
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.  
16207718 J.Hinnerwisch, B.G.Reid, W.A.Fenton, and A.L.Horwich (2005).
Roles of the N-domains of the ClpA unfoldase in binding substrate proteins and in stable complex formation with the ClpP protease.
  J Biol Chem, 280, 40838-40844.  
16061814 J.Shen, D.Gai, A.Patrick, W.B.Greenleaf, and X.S.Chen (2005).
The roles of the residues on the channel beta-hairpin and loop structures of simian virus 40 hexameric helicase.
  Proc Natl Acad Sci U S A, 102, 11248-11253.  
15983416 J.Wang, S.H.Rho, H.H.Park, and S.H.Eom (2005).
Correction of X-ray intensities from an HslV-HslU co-crystal containing lattice-translocation defects.
  Acta Crystallogr D Biol Crystallogr, 61, 932-941.
PDB code: 1yyf
15678420 M.Groll, M.Bochtler, H.Brandstetter, T.Clausen, and R.Huber (2005).
Molecular machines for protein degradation.
  Chembiochem, 6, 222-256.  
15802652 M.K.Azim, W.Goehring, H.K.Song, R.Ramachandran, M.Bochtler, and P.Goettig (2005).
Characterization of the HslU chaperone affinity for HslV protease.
  Protein Sci, 14, 1357-1362.  
15611053 M.Su'etsugu, T.R.Shimuta, T.Ishida, H.Kawakami, and T.Katayama (2005).
Protein associations in DnaA-ATP hydrolysis mediated by the Hda-replicase clamp complex.
  J Biol Chem, 280, 6528-6536.  
16162497 P.Beinker, S.Schlee, R.Auvula, and J.Reinstein (2005).
Biochemical coupling of the two nucleotide binding domains of ClpB: covalent linkage is not a prerequisite for chaperone activity.
  J Biol Chem, 280, 37965-37973.  
16072036 P.I.Hanson, and S.W.Whiteheart (2005).
AAA+ proteins: have engine, will work.
  Nat Rev Mol Cell Biol, 6, 519-529.  
15696175 R.E.Burton, T.A.Baker, and R.T.Sauer (2005).
Nucleotide-dependent substrate recognition by the AAA+ HslUV protease.
  Nat Struct Mol Biol, 12, 245-251.  
15829969 S.J.Riedl, W.Li, Y.Chao, R.Schwarzenbacher, and Y.Shi (2005).
Structure of the apoptotic protease-activating factor 1 bound to ADP.
  Nature, 434, 926-933.
PDB code: 1z6t
15181012 A.Y.Lee, C.H.Hsu, and S.H.Wu (2004).
Functional domains of Brevibacillus thermoruber lon protease for oligomerization and DNA binding: role of N-terminal and sensor and substrate discrimination domains.
  J Biol Chem, 279, 34903-34912.  
15208691 C.Schlieker, J.Weibezahn, H.Patzelt, P.Tessarz, C.Strub, K.Zeth, A.Erbse, J.Schneider-Mergener, J.W.Chin, P.G.Schultz, B.Bukau, and A.Mogk (2004).
Substrate recognition by the AAA+ chaperone ClpB.
  Nat Struct Mol Biol, 11, 607-615.  
15039430 D.M.Janse, B.Crosas, D.Finley, and G.M.Church (2004).
Localization to the proteasome is sufficient for degradation.
  J Biol Chem, 279, 21415-21420.  
15529165 F.Baneyx, and M.Mujacic (2004).
Recombinant protein folding and misfolding in Escherichia coli.
  Nat Biotechnol, 22, 1399-1408.  
15178690 J.M.Tkach, and J.R.Glover (2004).
Amino acid substitutions in the C-terminal AAA+ module of Hsp104 prevent substrate recognition by disrupting oligomerization and cause high temperature inactivation.
  J Biol Chem, 279, 35692-35701.  
14728719 J.Weibezahn, B.Bukau, and A.Mogk (2004).
Unscrambling an egg: protein disaggregation by AAA+ proteins.
  Microb Cell Fact, 3, 1.  
14962378 M.R.Maurizi, and D.Xia (2004).
Protein binding and disruption by Clp/Hsp100 chaperones.
  Structure, 12, 175-183.  
15031730 P.Laksanalamai, T.A.Whitehead, and F.T.Robb (2004).
Minimal protein-folding systems in hyperthermophilic archaea.
  Nat Rev Microbiol, 2, 315-324.  
15547284 R.Qamra, and S.C.Mande (2004).
Crystal structure of the 65-kilodalton heat shock protein, chaperonin 60.2, of Mycobacterium tuberculosis.
  J Bacteriol, 186, 8105-8113.
PDB code: 1sjp
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.  
15210950 T.Hishida, Y.W.Han, S.Fujimoto, H.Iwasaki, and H.Shinagawa (2004).
Direct evidence that a conserved arginine in RuvB AAA+ ATPase acts as an allosteric effector for the ATPase activity of the adjacent subunit in a hexamer.
  Proc Natl Acad Sci U S A, 101, 9573-9577.  
14978298 V.Akoev, E.P.Gogol, M.E.Barnett, and M.Zolkiewski (2004).
Nucleotide-induced switch in oligomerization of the AAA+ ATPase ClpB.
  Protein Sci, 13, 567-574.  
12582167 A.Johnson, and M.O'Donnell (2003).
Ordered ATP hydrolysis in the gamma complex clamp loader AAA+ machine.
  J Biol Chem, 278, 14406-14413.  
12624113 A.Mogk, C.Schlieker, C.Strub, W.Rist, J.Weibezahn, and B.Bukau (2003).
Roles of individual domains and conserved motifs of the AAA+ chaperone ClpB in oligomerization, ATP hydrolysis, and chaperone activity.
  J Biol Chem, 278, 17615-17624.  
12774115 D.Li, R.Zhao, W.Lilyestrom, D.Gai, R.Zhang, J.A.DeCaprio, E.Fanning, A.Jochimiak, G.Szakonyi, and X.S.Chen (2003).
Structure of the replicative helicase of the oncoprotein SV40 large tumour antigen.
  Nature, 423, 512-518.
PDB code: 1n25
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
12622725 F.Hayashi, H.Suzuki, R.Iwase, T.Uzumaki, A.Miyake, J.R.Shen, K.Imada, Y.Furukawa, K.Yonekura, K.Namba, and M.Ishiura (2003).
ATP-induced hexameric ring structure of the cyanobacterial circadian clock protein KaiC.
  Genes Cells, 8, 287-296.  
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
12906833 J.A.James, C.R.Escalante, M.Yoon-Robarts, T.A.Edwards, R.M.Linden, and A.K.Aggarwal (2003).
Crystal structure of the SF3 helicase from adeno-associated virus type 2.
  Structure, 11, 1025-1035.
PDB code: 1s9h
12623019 J.Li, and B.Sha (2003).
Crystal structure of the E. coli Hsp100 ClpB N-terminal domain.
  Structure, 11, 323-328.  
14690443 K.Kustedjo, S.Deechongkit, J.W.Kelly, and B.F.Cravatt (2003).
Recombinant expression, purification, and comparative characterization of torsinA and its torsion dystonia-associated variant Delta E-torsinA.
  Biochemistry, 42, 15333-15341.  
14525985 L.W.Donaldson, U.Wojtyra, and W.A.Houry (2003).
Solution structure of the dimeric zinc binding domain of the chaperone ClpX.
  J Biol Chem, 278, 48991-48996.
PDB code: 1ovx
12672453 M.Groll, and R.Huber (2003).
Substrate access and processing by the 20S proteasome core particle.
  Int J Biochem Cell Biol, 35, 606-616.  
14675543 M.Groll, and T.Clausen (2003).
Molecular shredders: how proteasomes fulfill their role.
  Curr Opin Struct Biol, 13, 665-673.  
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.  
12657045 S.A.Joshi, T.A.Baker, and R.T.Sauer (2003).
C-terminal domain mutations in ClpX uncouple substrate binding from an engagement step required for unfolding.
  Mol Microbiol, 48, 67-76.  
14570582 S.Gottesman (2003).
Proteolysis in bacterial regulatory circuits.
  Annu Rev Cell Dev Biol, 19, 565-587.  
14561776 S.Y.Lee, A.De La Torre, D.Yan, S.Kustu, B.T.Nixon, and D.E.Wemmer (2003).
Regulation of the transcriptional activator NtrC1: structural studies of the regulatory and AAA+ ATPase domains.
  Genes Dev, 17, 2552-2563.
PDB codes: 1ny5 1ny6
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.  
14506706 W.Gartner, J.Rossbacher, B.Zierhut, T.Daneva, W.Base, M.Weissel, W.Waldhäusl, M.S.Pasternack, and L.Wagner (2003).
The ATP-dependent helicase RUVBL1/TIP49a associates with tubulin during mitosis.
  Cell Motil Cytoskeleton, 56, 79-93.  
12655133 W.Sakamoto (2003).
Leaf-variegated mutations and their responsible genes in Arabidopsis thaliana.
  Genes Genet Syst, 78, 1-9.  
14526036 Y.K.Wang, S.Park, B.T.Nixon, and T.R.Hoover (2003).
Nucleotide-dependent conformational changes in the sigma54-dependent activator DctD.
  J Bacteriol, 185, 6215-6219.  
12670962 Y.Y.Lee, C.F.Chang, C.L.Kuo, M.C.Chen, C.H.Yu, P.I.Lin, and W.F.Wu (2003).
Subunit oligomerization and substrate recognition of the Escherichia coli ClpYQ (HslUV) protease implicated by in vivo protein-protein interactions in the yeast two-hybrid system.
  J Bacteriol, 185, 2393-2401.  
11983167 A.G.Cashikar, E.C.Schirmer, D.A.Hattendorf, J.R.Glover, M.S.Ramakrishnan, D.M.Ware, and S.L.Lindquist (2002).
Defining a pathway of communication from the C-terminal peptide binding domain to the N-terminal ATPase domain in a AAA protein.
  Mol Cell, 9, 751-760.  
12357035 A.Hansson, R.D.Willows, T.H.Roberts, and M.Hansson (2002).
Three semidominant barley mutants with single amino acid substitutions in the smallest magnesium chelatase subunit form defective AAA+ hexamers.
  Proc Natl Acad Sci U S A, 99, 13944-13949.  
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.  
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.  
11867765 D.A.Hattendorf, and S.L.Lindquist (2002).
Analysis of the AAA sensor-2 motif in the C-terminal ATPase domain of Hsp104 with a site-specific fluorescent probe of nucleotide binding.
  Proc Natl Acad Sci U S A, 99, 2732-2737.  
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.  
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
11748238 F.X.Gomis-Rüth, G.Moncalían, F.de la Cruz, and M.Coll (2002).
Conjugative plasmid protein TrwB, an integral membrane type IV secretion system coupling protein. Detailed structural features and mapping of the active site cleft.
  J Biol Chem, 277, 7556-7566.  
12455966 H.D.Ulrich (2002).
Degradation or maintenance: actions of the ubiquitin system on eukaryotic chromatin.
  Eukaryot Cell, 1, 1.  
12377127 H.Niwa, D.Tsuchiya, H.Makyio, M.Yoshida, and K.Morikawa (2002).
Hexameric ring structure of the ATPase domain of the membrane-integrated metalloprotease FtsH from Thermus thermophilus HB8.
  Structure, 10, 1415-1423.
PDB codes: 1ixz 1iy0 1iy1 1iy2
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.  
12234917 J.P.Erzberger, M.M.Pirruccello, and J.M.Berger (2002).
The structure of bacterial DnaA: implications for general mechanisms underlying DNA replication initiation.
  EMBO J, 21, 4763-4773.
PDB code: 1l8q
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
12220194 M.E.Barnett, and M.Zolkiewski (2002).
Site-directed mutagenesis of conserved charged amino acid residues in ClpB from Escherichia coli.
  Biochemistry, 41, 11277-11283.  
11827963 N.Takahashi, S.Tsutsumi, T.Tsuchiya, B.Stillman, and T.Mizushima (2002).
Functions of sensor 1 and sensor 2 regions of Saccharomyces cerevisiae Cdc6p in vivo and in vitro.
  J Biol Chem, 277, 16033-16040.  
12351638 P.Beinker, S.Schlee, Y.Groemping, R.Seidel, and J.Reinstein (2002).
The N terminus of ClpB from Thermus thermophilus is not essential for the chaperone activity.
  J Biol Chem, 277, 47160-47166.  
12209147 P.Chène (2002).
ATPases as drug targets: learning from their structure.
  Nat Rev Drug Discov, 1, 665-673.  
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.  
11839737 S.Nishida, K.Fujimitsu, K.Sekimizu, T.Ohmura, T.Ueda, and T.Katayama (2002).
A nucleotide switch in the Escherichia coli DnaA protein initiates chromosomal replication: evidnece from a mutant DnaA protein defective in regulatory ATP hydrolysis in vitro and in vivo.
  J Biol Chem, 277, 14986-14995.  
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.  
12164771 T.Perls, and A.Puca (2002).
The genetics of aging-- implications for pharmacogenomics.
  Pharmacogenomics, 3, 469-484.  
11967375 V.Tek, and M.Zolkiewski (2002).
Stability and interactions of the amino-terminal domain of ClpB from Escherichia coli.
  Protein Sci, 11, 1192-1198.  
12167156 W.Sakamoto, T.Tamura, Y.Hanba-Tomita, and M.Murata (2002).
The VAR1 locus of Arabidopsis encodes a chloroplastic FtsH and is responsible for leaf variegation in the mutant alleles.
  Genes Cells, 7, 769-780.  
11959502 X.Zhang, F.Beuron, and P.S.Freemont (2002).
Machinery of protein folding and unfolding.
  Curr Opin Struct Biol, 12, 231-238.  
12180911 X.Zhang, M.Chaney, S.R.Wigneshweraraj, J.Schumacher, P.Bordes, W.Cannon, and M.Buck (2002).
Mechanochemical ATPases and transcriptional activation.
  Mol Microbiol, 45, 895-903.  
11741950 Y.H.Watanabe, K.Motohashi, and M.Yoshida (2002).
Roles of the two ATP binding sites of ClpB from Thermus thermophilus.
  J Biol Chem, 277, 5804-5809.  
11468391 C.B.Trame, and D.B.McKay (2001).
Structure of Haemophilus influenzae HslU protein in crystals with one-dimensional disorder twinning.
  Acta Crystallogr D Biol Crystallogr, 57, 1079-1090.
PDB codes: 1g41 1im2
11316608 D.J.Asai, and M.P.Koonce (2001).
The dynein heavy chain: structure, mechanics and evolution.
  Trends Cell Biol, 11, 196-202.  
11158570 E.C.Schirmer, D.M.Ware, C.Queitsch, A.S.Kowal, and S.L.Lindquist (2001).
Subunit interactions influence the biochemical and biological properties of Hsp104.
  Proc Natl Acad Sci U S A, 98, 914-919.  
11179229 E.Krüger, D.Zühlke, E.Witt, H.Ludwig, and M.Hecker (2001).
Clp-mediated proteolysis in Gram-positive bacteria is autoregulated by the stability of a repressor.
  EMBO J, 20, 852-863.  
11250194 G.Mocz, and I.R.Gibbons (2001).
Model for the motor component of dynein heavy chain based on homology to the AAA family of oligomeric ATPases.
  Structure, 9, 93.
PDB code: 1hn5
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.  
11375526 J.Li, and B.Sha (2001).
Cloning, expression, purification and preliminary X-ray crystallographic studies of Escherichia coli Hsp100 ClpB nucleotide-binding domain 1 (NBD1).
  Acta Crystallogr D Biol Crystallogr, 57, 909-911.  
11717522 J.Li, and B.Sha (2001).
Cloning, expression, purification and preliminary X-ray crystallographic studies of Escherichia coli Hsp100 ClpB N-terminal domain.
  Acta Crystallogr D Biol Crystallogr, 57, 1933-1935.  
11716297 J.R.Glover, and J.M.Tkach (2001).
Crowbars and ratchets: hsp100 chaperones as tools in reversing protein aggregation.
  Biochem Cell Biol, 79, 557-568.  
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
11251810 K.Karata, C.S.Verma, A.J.Wilkinson, and T.Ogura (2001).
Probing the mechanism of ATP hydrolysis and substrate translocation in the AAA protease FtsH by modelling and mutagenesis.
  Mol Microbiol, 39, 890-903.  
11722737 K.Turgay, M.Persuh, J.Hahn, and D.Dubnau (2001).
Roles of the two ClpC ATP binding sites in the regulation of competence and the stress response.
  Mol Microbiol, 42, 717-727.  
11171970 K.Yamada, N.Kunishima, K.Mayanagi, T.Ohnishi, T.Nishino, H.Iwasaki, H.Shinagawa, and K.Morikawa (2001).
Crystal structure of the Holliday junction migration motor protein RuvB from Thermus thermophilus HB8.
  Proc Natl Acad Sci U S A, 98, 1442-1447.
PDB code: 1hqc
11717526 M.C.Sousa, and D.B.McKay (2001).
Structure of Haemophilus influenzae HslV protein at 1.9 A resolution, revealing a cation-binding site near the catalytic site.
  Acta Crystallogr D Biol Crystallogr, 57, 1950-1954.
PDB code: 1jjw
11163235 S.Dalal, and P.I.Hanson (2001).
Membrane traffic: what drives the AAA motor?
  Cell, 104, 5-8.  
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.  
11016885 A.J.Rivett, and R.C.Gardner (2000).
Proteasome inhibitors: from in vitro uses to clinical trials.
  J Pept Sci, 6, 478-488.  
11114186 H.K.Song, C.Hartmann, R.Ramachandran, M.Bochtler, R.Behrendt, L.Moroder, and R.Huber (2000).
Mutational studies on HslU and its docking mode with HslV.
  Proc Natl Acad Sci U S A, 97, 14103-14108.
PDB code: 1e94
11009422 I.Levchenko, M.Seidel, R.T.Sauer, and T.A.Baker (2000).
A specificity-enhancing factor for the ClpXP degradation machine.
  Science, 289, 2354-2356.  
11163220 I.Rouiller, V.M.Butel, M.Latterich, R.A.Milligan, and E.M.Wilson-Kubalek (2000).
A major conformational change in p97 AAA ATPase upon ATP binding.
  Mol Cell, 6, 1485-1490.  
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.  
11106733 M.C.Sousa, C.B.Trame, H.Tsuruta, S.M.Wilbanks, V.S.Reddy, and D.B.McKay (2000).
Crystal and solution structures of an HslUV protease-chaperone complex.
  Cell, 103, 633-643.
PDB codes: 1g3i 1g3k
10982797 M.E.Barnett, A.Zolkiewska, and M.Zolkiewski (2000).
Structure and activity of ClpB from Escherichia coli. Role of the amino-and -carboxyl-terminal domains.
  J Biol Chem, 275, 37565-37571.  
10893253 R.D.Vale (2000).
AAA proteins. Lords of the ring.
  J Cell Biol, 150, F13-F19.  
10830160 R.Verma, and R.J.Deshaies (2000).
A proteasome howdunit: the case of the missing signal.
  Cell, 101, 341-344.  
  11029046 R.Verma, S.Chen, R.Feldman, D.Schieltz, J.Yates, J.Dohmen, and R.J.Deshaies (2000).
Proteasomal proteomics: identification of nucleotide-sensitive proteasome-interacting proteins by mass spectrometric analysis of affinity-purified proteasomes.
  Mol Biol Cell, 11, 3425-3439.  
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.  
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