PDBsum entry 1g4b

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protein Protein-protein interface(s) links
Chaperone/hydrolase PDB id
Protein chains
393 a.a. *
173 a.a. *
* Residue conservation analysis
PDB id:
Name: Chaperone/hydrolase
Title: Crystal structures of the hslvu peptidase-atpase complex reveal an atp-dependent proteolysis mechanism
Structure: Atp-dependent hsl protease atp-binding subunit hslu. Chain: e, f, k, l. Synonym: heat shock locus hslu atpase. Engineered: yes. Atp-dependent protease hslv. Chain: m, n, o, p. Synonym: heat shock locus hslv peptidase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: 24mer (from PDB file)
7.00Å     R-factor:   0.401     R-free:   0.432
Authors: 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,S.H.Eom
Key ref:
J.Wang et al. (2001). Crystal structures of the HslVU peptidase-ATPase complex reveal an ATP-dependent proteolysis mechanism. Structure, 9, 177-184. PubMed id: 11250202 DOI: 10.1016/S0969-2126(01)00570-6
26-Oct-00     Release date:   21-Feb-01    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P0A6H5  (HSLU_ECOLI) -  ATP-dependent protease ATPase subunit HslU
443 a.a.
393 a.a.
Protein chains
Pfam   ArchSchema ?
P0A7B8  (HSLV_ECOLI) -  ATP-dependent protease subunit HslV
176 a.a.
173 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class: Chains M, O, P: E.C.  - HslU--HslV peptidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   5 terms 
  Biological process     metabolic process   8 terms 
  Biochemical function     catalytic activity     12 terms  


DOI no: 10.1016/S0969-2126(01)00570-6 Structure 9:177-184 (2001)
PubMed id: 11250202  
Crystal structures of the HslVU peptidase-ATPase complex reveal an ATP-dependent proteolysis mechanism.
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, S.H.Eom.
BACKGROUND: The bacterial heat shock locus HslU ATPase and HslV peptidase together form an ATP-dependent HslVU protease. Bacterial HslVU is a homolog of the eukaryotic 26S proteasome. Crystallographic studies of HslVU should provide an understanding of ATP-dependent protein unfolding, translocation, and proteolysis by this and other ATP-dependent proteases. RESULTS: We present a 3.0 A resolution crystal structure of HslVU with an HslU hexamer bound at one end of an HslV dodecamer. The structure shows that the central pores of the ATPase and peptidase are next to each other and aligned. The central pore of HslU consists of a GYVG motif, which is conserved among protease-associated ATPases. The binding of one HslU hexamer to one end of an HslV dodecamer in the 3.0 A resolution structure opens both HslV central pores and induces asymmetric changes in HslV. CONCLUSIONS: Analysis of nucleotide binding induced conformational changes in the current and previous HslU structures suggests a protein unfolding-coupled translocation mechanism. In this mechanism, unfolded polypeptides are threaded through the aligned pores of the ATPase and peptidase and translocated into the peptidase central chamber.
  Selected figure(s)  
Figure 1.
Figure 1. The Structures of HslVU(a) A composite-omit electron density map (cyan, contoured at 1s) at 3.0 Å resolution reveals that the bound dADP (yellow) is in an anti conformation, not syn, as in a previously determined structure (AMPPNP, magenta). This map was generated before dADP was built into the model.(b) The HslVU complex in the asymmetric U[6]V[6]V[6] configuration. Parts of HslU domain I could not be built into the final electron density and are indicated by spheres for their approximate locations.(c) The HslVU structure in the symmetric U[6]V[6]V[6]U[6] configuration. The orientation of the complexes in (1b) and (1c) differs by 30°

  The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 177-184) copyright 2001.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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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.
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PDB codes: 3ktg 3kth 3kti 3ktj 3ktk
20203624 F.Striebel, M.Hunkeler, H.Summer, and E.Weber-Ban (2010).
The mycobacterial Mpa-proteasome unfolds and degrades pupylated substrates by engaging Pup's N-terminus.
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Structural basis for the unfolding of anthrax lethal factor by protective antigen oligomers.
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PDB code: 3kwv
19926290 H.X.Zhou, and J.A.McCammon (2010).
The gates of ion channels and enzymes.
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20541423 N.Gallastegui, and M.Groll (2010).
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20404203 S.Lee, B.Sielaff, J.Lee, and F.T.Tsai (2010).
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The crystal structure of apo-FtsH reveals domain movements necessary for substrate unfolding and translocation.
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PDB code: 3kds
19362814 F.Striebel, W.Kress, and E.Weber-Ban (2009).
Controlled destruction: AAA+ ATPases in protein degradation from bacteria to eukaryotes.
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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.
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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.
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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
19008106 S.M.Doyle, and S.Wickner (2009).
Hsp104 and ClpB: protein disaggregating machines.
  Trends Biochem Sci, 34, 40-48.  
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.  
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.  
18359303 I.Lee, and C.K.Suzuki (2008).
Functional mechanics of the ATP-dependent Lon protease- lessons from endogenous protein and synthetic peptide substrates.
  Biochim Biophys Acta, 1784, 727-735.  
18582897 J.A.Yakamavich, T.A.Baker, and R.T.Sauer (2008).
Asymmetric nucleotide transactions of the HslUV protease.
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18466635 J.Snider, G.Thibault, and W.A.Houry (2008).
The AAA+ superfamily of functionally diverse proteins.
  Genome Biol, 9, 216.  
18923516 J.Zimmer, Y.Nam, and T.A.Rapoport (2008).
Structure of a complex of the ATPase SecA and the protein-translocation channel.
  Nature, 455, 936-943.
PDB codes: 3din 3dl8
18923526 K.J.Erlandson, S.B.Miller, Y.Nam, A.R.Osborne, J.Zimmer, and T.A.Rapoport (2008).
A role for the two-helix finger of the SecA ATPase in protein translocation.
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18929572 M.D.Gonciarz, F.G.Whitby, D.M.Eckert, C.Kieffer, A.Heroux, W.I.Sundquist, and C.P.Hill (2008).
Biochemical and structural studies of yeast Vps4 oligomerization.
  J Mol Biol, 384, 878-895.
PDB codes: 3eie 3eih
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.  
18421140 S.H.Kim, G.B.Kang, H.E.Song, S.J.Park, M.H.Bea, and S.H.Eom (2008).
Structural studies on Helicobacter pyloriATP-dependent protease, FtsH.
  J Synchrotron Radiat, 15, 208-210.
PDB codes: 2r62 2r65
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
18276129 T.Inobe, and A.Matouschek (2008).
Protein targeting to ATP-dependent proteases.
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18985068 T.Inobe, D.A.Kraut, and A.Matouschek (2008).
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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.  
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.
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17897320 S.R.White, and B.Lauring (2007).
AAA+ ATPases: achieving diversity of function with conserved machinery.
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17389232 S.R.White, K.J.Evans, J.Lary, J.L.Cole, and B.Lauring (2007).
Recognition of C-terminal amino acids in tubulin by pore loops in Spastin is important for microtubule severing.
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17012286 A.F.Neuwald (2006).
Hypothesis: bacterial clamp loader ATPase activation through DNA-dependent repositioning of the catalytic base and of a trans-acting catalytic threonine.
  Nucleic Acids Res, 34, 5280-5290.  
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.
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17082771 M.J.Pearce, P.Arora, R.A.Festa, S.M.Butler-Wu, R.S.Gokhale, and K.H.Darwin (2006).
Identification of substrates of the Mycobacterium tuberculosis proteasome.
  EMBO J, 25, 5423-5432.  
17021930 M.X.Ruiz-González, and I.Marín (2006).
Proteasome-related HslU and HslV genes typical of eubacteria are widespread in eukaryotes.
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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
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.  
16236712 A.Gerega, B.Rockel, J.Peters, T.Tamura, W.Baumeister, and P.Zwickl (2005).
VAT, the thermoplasma homolog of mammalian p97/VCP, is an N domain-regulated protein unfoldase.
  J Biol Chem, 280, 42856-42862.  
16193069 A.Scott, H.Y.Chung, M.Gonciarz-Swiatek, G.C.Hill, F.G.Whitby, J.Gaspar, J.M.Holton, R.Viswanathan, S.Ghaffarian, C.P.Hill, and W.I.Sundquist (2005).
Structural and mechanistic studies of VPS4 proteins.
  EMBO J, 24, 3658-3669.
PDB code: 1xwi
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.  
15689967 J.Shorter, and S.Lindquist (2005).
Navigating the ClpB channel to solution.
  Nat Struct Mol Biol, 12, 4-6.  
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
16201868 J.Weibezahn, C.Schlieker, P.Tessarz, A.Mogk, and B.Bukau (2005).
Novel insights into the mechanism of chaperone-assisted protein disaggregation.
  Biol Chem, 386, 739-744.  
15910274 K.Ito, and Y.Akiyama (2005).
Cellular functions, mechanism of action, and regulation of FtsH protease.
  Annu Rev Microbiol, 59, 211-231.  
16072036 P.I.Hanson, and S.W.Whiteheart (2005).
AAA+ proteins: have engine, will work.
  Nat Rev Mol Cell Biol, 6, 519-529.  
14738756 A.Mogk, and B.Bukau (2004).
Molecular chaperones: structure of a protein disaggregase.
  Curr Biol, 14, R78-R80.  
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.  
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.  
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.  
15550247 J.Weibezahn, P.Tessarz, C.Schlieker, R.Zahn, Z.Maglica, S.Lee, H.Zentgraf, E.U.Weber-Ban, D.A.Dougan, F.T.Tsai, A.Mogk, and B.Bukau (2004).
Thermotolerance requires refolding of aggregated proteins by substrate translocation through the central pore of ClpB.
  Cell, 119, 653-665.  
14962378 M.R.Maurizi, and D.Xia (2004).
Protein binding and disruption by Clp/Hsp100 chaperones.
  Structure, 12, 175-183.  
15128736 R.Lum, J.M.Tkach, E.Vierling, and J.R.Glover (2004).
Evidence for an unfolding/threading mechanism for protein disaggregation by Saccharomyces cerevisiae Hsp104.
  J Biol Chem, 279, 29139-29146.  
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.  
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.  
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
12511496 I.Nagy, T.Banerjee, T.Tamura, G.Schoofs, A.Gils, P.Proost, N.Tamura, W.Baumeister, and R.De Mot (2003).
Characterization of a novel intracellular endopeptidase of the alpha/beta hydrolase family from Streptomyces coelicolor A3(2).
  J Bacteriol, 185, 496-503.  
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
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
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.  
14635249 P.C.Burrows (2003).
Investigating protein-protein interfaces in bacterial transcription complexes: a fragmentation approach.
  Bioessays, 25, 1150-1153.  
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.  
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
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.  
12112691 A.Teplyakov, G.Obmolova, M.Tordova, N.Thanki, N.Bonander, E.Eisenstein, A.J.Howard, and G.L.Gilliland (2002).
Crystal structure of the YjeE protein from Haemophilus influenzae: a putative Atpase involved in cell wall synthesis.
  Proteins, 48, 220-226.
PDB codes: 1fl9 1htw
12270919 A.V.Kajava (2002).
What curves alpha-solenoids? Evidence for an alpha-helical toroid structure of Rpn1 and Rpn2 proteins of the 26 S proteasome.
  J Biol Chem, 277, 49791-49798.  
12006565 A.Zakalskiy, G.Högenauer, T.Ishikawa, E.Wehrschütz-Sigl, F.Wendler, D.Teis, G.Zisser, A.C.Steven, and H.Bergler (2002).
Structural and enzymatic properties of the AAA protein Drg1p from Saccharomyces cerevisiae. Decoupling of intracellular function from ATPase activity and hexamerization.
  J Biol Chem, 277, 26788-26795.  
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
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.  
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.  
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.  
11959502 X.Zhang, F.Beuron, and P.S.Freemont (2002).
Machinery of protein folding and unfolding.
  Curr Opin Struct Biol, 12, 231-238.  
12399180 Z.Adam, and A.K.Clarke (2002).
Cutting edge of chloroplast proteolysis.
  Trends Plant Sci, 7, 451-456.  
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
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
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