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PDBsum entry 1e94

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protein ligands Protein-protein interface(s) links
Chaperone PDB id
1e94
Jmol
Contents
Protein chains
174 a.a. *
408 a.a. *
Ligands
ANP ×2
Waters ×286
* Residue conservation analysis
PDB id:
1e94
Name: Chaperone
Title: Hslv-hslu from e.Coli
Structure: Heat shock protein hslv. Chain: a, b, c, d. Synonym: hslv. Engineered: yes. Heat shock protein hslu. Chain: e, f. Synonym: hslu. Engineered: yes
Source: Escherichia coli. Organism_taxid: 469008. Strain: bl21(de3). Cellular_location: cytoplasm. Plasmid: pet12b. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Homo-Dodecamer (from PDB file)
Resolution:
2.8Å     R-factor:   0.254     R-free:   0.304
Authors: H.K.Song,C.Hartmann,R.Ravishankar,M.Bochtler
Key ref:
H.K.Song et al. (2000). Mutational studies on HslU and its docking mode with HslV. Proc Natl Acad Sci U S A, 97, 14103-14108. PubMed id: 11114186 DOI: 10.1073/pnas.250491797
Date:
07-Oct-00     Release date:   17-Nov-00    
Supersedes: 1doo
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A7B8  (HSLV_ECOLI) -  ATP-dependent protease subunit HslV
Seq:
Struc:
176 a.a.
174 a.a.
Protein chains
Pfam   ArchSchema ?
P0A6H5  (HSLU_ECOLI) -  ATP-dependent protease ATPase subunit HslU
Seq:
Struc:
443 a.a.
408 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: E.C.3.4.25.2  - 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: 10.1073/pnas.250491797 Proc Natl Acad Sci U S A 97:14103-14108 (2000)
PubMed id: 11114186  
 
 
Mutational studies on HslU and its docking mode with HslV.
H.K.Song, C.Hartmann, R.Ramachandran, M.Bochtler, R.Behrendt, L.Moroder, R.Huber.
 
  ABSTRACT  
 
HslVU is an ATP-dependent prokaryotic protease complex. Despite detailed crystal and molecular structure determinations of free HslV and HslU, the mechanism of ATP-dependent peptide and protein hydrolysis remained unclear, mainly because the productive complex of HslV and HslU could not be unambiguously identified from the crystal data. In the crystalline complex, the I domains of HslU interact with HslV. Observations based on electron microscopy data were interpreted in the light of the crystal structure to indicate an alternative mode of association with the intermediate domains away from HslV. By generation and analysis of two dozen HslU mutants, we find that the amidolytic and caseinolytic activities of HslVU are quite robust to mutations on both alternative docking surfaces on HslU. In contrast, HslVU activity against the maltose-binding protein-SulA fusion protein depends on the presence of the I domain and is also sensitive to mutations in the N-terminal and C-terminal domains of HslU. Mutational studies around the hexameric pore of HslU seem to show that it is involved in the recognition/translocation of maltose-binding protein-SulA but not of chromogenic small substrates and casein. ATP-binding site mutations, among other things, confirm the essential role of the "sensor arginine" (R393) and the "arginine finger" (R325) in the ATPase action of HslU and demonstrate an important role for E321. Additionally, we report a better refined structure of the HslVU complex crystallized along with resorufin-labeled casein.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Representation of the electrostatic potential surfaces of HslV (Left) and HslU (Center) involved in the EM mode of docking. Negatively charged regions are in red, and positively charged regions are in blue. Sites of mutations in the HslU (Right). Numbers 1 (green) and 3 (pink) mark sites of pentaglycine insertions after residues 264 and 387 as well as changes of surface charges (E266Q; E266Q/E385K), 2 (blue) marks the site of introduction of a bulky side chain (I312W), and 4 (red) marks the site of a charge reversal (E436K/D437K). The hexamer pore is colored in yellow. This figure was drawn by using GRASP (28).
Figure 3.
Fig. 3. Sites of mutations in the hexamer pore. Side-chain atoms (yellow) are shown only in one subunit for clarity. Mutation sites in the hexamer pore are colored in pink. Top view of HslU (Left). Side view of the central pore of HslU hexamer (Right). Two subunits from the ring nearest to the reader are removed to expose the interior. This figure was drawn by using GRASP (28).
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21460456 E.Krissinel (2011).
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20693326 E.Marquenet, and E.Richet (2010).
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20129058 M.Makowska-Grzyska, and J.M.Kaguni (2010).
Primase directs the release of DnaC from DnaB.
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19714768 S.Zietkiewicz, M.J.Slusarz, R.Slusarz, K.Liberek, and S.Rodziewicz-Motowidło (2010).
Conformational stability of the full-atom hexameric model of the ClpB chaperone from Escherichia coli.
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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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19609260 J.Kirstein, N.Molière, D.A.Dougan, and K.Turgay (2009).
Adapting the machine: adaptor proteins for Hsp100/Clp and AAA+ proteases.
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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.
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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.
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19748354 S.Augustin, F.Gerdes, S.Lee, F.T.Tsai, T.Langer, and T.Tatsuta (2009).
An intersubunit signaling network coordinates ATP hydrolysis by m-AAA proteases.
  Mol Cell, 35, 574-585.  
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.  
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.  
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.  
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.  
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.  
17873068 K.Hupert-Kocurek, J.M.Sage, M.Makowska-Grzyska, and J.M.Kaguni (2007).
Genetic method to analyze essential genes of Escherichia coli.
  Appl Environ Microbiol, 73, 7075-7082.  
17261594 M.Graef, G.Seewald, and T.Langer (2007).
Substrate recognition by AAA+ ATPases: distinct substrate binding modes in ATP-dependent protease Yme1 of the mitochondrial intermembrane space.
  Mol Cell Biol, 27, 2476-2485.  
17897320 S.R.White, and B.Lauring (2007).
AAA+ ATPases: achieving diversity of function with conserved machinery.
  Traffic, 8, 1657-1667.  
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
16753031 J.M.Kaguni (2006).
DnaA: controlling the initiation of bacterial DNA replication and more.
  Annu Rev Microbiol, 60, 351-375.  
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.  
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
16307477 C.Schlieker, H.Zentgraf, P.Dersch, and A.Mogk (2005).
ClpV, a unique Hsp100/Clp member of pathogenic proteobacteria.
  Biol Chem, 386, 1115-1127.  
16337593 D.M.Smith, G.Kafri, Y.Cheng, D.Ng, T.Walz, and A.L.Goldberg (2005).
ATP binding to PAN or the 26S ATPases causes association with the 20S proteasome, gate opening, and translocation of unfolded proteins.
  Mol Cell, 20, 687-698.  
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.  
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.  
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.  
14738756 A.Mogk, and B.Bukau (2004).
Molecular chaperones: structure of a protein disaggregase.
  Curr Biol, 14, R78-R80.  
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.  
15289463 E.A.Abbate, J.M.Berger, and M.R.Botchan (2004).
The X-ray structure of the papillomavirus helicase in complex with its molecular matchmaker E2.
  Genes Dev, 18, 1981-1996.
PDB code: 1tue
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.  
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.  
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.  
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.  
15153108 V.Lake, U.Olsson, R.D.Willows, and M.Hansson (2004).
ATPase activity of magnesium chelatase subunit I is required to maintain subunit D in vivo.
  Eur J Biochem, 271, 2182-2188.  
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
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.  
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.  
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.  
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
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.  
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
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.  
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.  
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
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
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.  
11473577 T.Ogura, and A.J.Wilkinson (2001).
AAA+ superfamily ATPases: common structure--diverse function.
  Genes Cells, 6, 575-597.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.