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PDBsum entry 1ned
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Hydrolase PDB id
1ned

 

 

 

 

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Contents
Protein chains
180 a.a. *
* Residue conservation analysis
PDB id:
1ned
Name: Hydrolase
Title: Crystal structure of hslv (clpq) at 3.8 angstroms resolution
Structure: Hslv. Chain: a, b, c. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Strain: xl-1 blue. Cellular_location: cytoplasm. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dodecamer (from PDB file)
Resolution:
3.80Å     R-factor:   0.256     R-free:   0.315
Authors: M.Bochtler,L.Ditzel,M.Groll,R.Huber
Key ref:
M.Bochtler et al. (1997). Crystal structure of heat shock locus V (HslV) from Escherichia coli. Proc Natl Acad Sci U S A, 94, 6070-6074. PubMed id: 9177170 DOI: 10.1073/pnas.94.12.6070
Date:
04-Apr-97     Release date:   08-Apr-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A7B8  (HSLV_ECOLI) -  ATP-dependent protease subunit HslV from Escherichia coli (strain K12)
Seq:
Struc: 		176 a.a.
180 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.25.2  - HslU--HslV peptidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
DOI no: 10.1073/pnas.94.12.6070 Proc Natl Acad Sci U S A 94:6070-6074 (1997)
PubMed id: 9177170  
 
 
Crystal structure of heat shock locus V (HslV) from Escherichia coli.
M.Bochtler, L.Ditzel, M.Groll, R.Huber.
 
  ABSTRACT  
 
Heat shock locus V (HslV; also called ClpQ) is the proteolytic core of the ATP-dependent protease HslVU in Escherichia coli. It has sequence similarity with the beta-type subunits of the eukaryotic and archaebacterial proteasomes. Unlike these particles, which display 72-point symmetry, it is a dimer of hexamers with 62-point symmetry. The crystal structure of HslV at 3.8-A resolution, determined by isomorphous replacement and symmetry averaging, shows that in spite of the different symmetry of the particle, the fold and the contacts between subunits are conserved. A tripeptide aldehyde inhibitor, acetyl-Leu-Leu-norleucinal, binds to the N-terminal threonine residue of HslV, probably as a hemiacetal, relating HslV also functionally to the proteasomes of archaea and eukaryotes.
 
  Selected figure(s)  
 
Figure 5.
Fig. 5. Overlay of HslV (red) with the T. acidophilum -subunit (green) with bound calpain inhibitors. The secondary structural elements are labeled. 		Figure 6.
Fig. 6. Overlay of one hexameric ring of HslV (red) with one heptameric ring of T. acidophilum -subunits (green).
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20541423 N.Gallastegui, and M.Groll (2010).
The 26S proteasome: assembly and function of a destructive machine.
  Trends Biochem Sci, 35, 634-642.  
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
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.  
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.  
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.  
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.  
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.  
18389302 R.E.Valas, and P.E.Bourne (2008).
Rethinking proteasome evolution: two novel bacterial proteasomes.
  J Mol Evol, 66, 494-504.  
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
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.  
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.  
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.  
17157318 Y.Wang, and H.C.Guo (2007).
Crystallographic snapshot of a productive glycosylasparaginase-substrate complex.
  J Mol Biol, 366, 82-92.
PDB code: 2gl9
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.  
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
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.  
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.  
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.  
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.  
16263929 R.Sprangers, A.Gribun, P.M.Hwang, W.A.Houry, and L.E.Kay (2005).
Quantitative NMR spectroscopy of supramolecular complexes: dynamic side pores in ClpP are important for product release.
  Proc Natl Acad Sci U S A, 102, 16678-16683.  
16041125 S.Yamamoto, Y.Otsuka, G.Borjigin, K.Masuda, Y.Ikeuchi, T.Nishiumi, and A.Suzuki (2005).
Effects of a high-pressure treatment on the activity and structure of rabbit muscle proteasome.
  Biosci Biotechnol Biochem, 69, 1239-1247.  
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.  
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.  
12948749 J.A.Maupin-Furlow, S.J.Kaczowka, C.J.Reuter, K.Zuobi-Hasona, and M.A.Gil (2003).
Archaeal proteasomes: potential in metabolic engineering.
  Metab Eng, 5, 151-163.  
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.  
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.  
  15803660 D.E.Ward, K.R.Shockley, L.S.Chang, R.D.Levy, J.K.Michel, S.B.Conners, and R.M.Kelly (2002).
Proteolysis in hyperthermophilic microorganisms.
  Archaea, 1, 63-74.  
12044173 F.C.Portaro, M.A.Hayashi, L.J.De Arauz, M.S.Palma, M.T.Assakura, C.L.Silva, and A.C.de Camargo (2002).
The Mycobacterium leprae hsp65 displays proteolytic activity. Mutagenesis studies indicate that the M. leprae hsp65 proteolytic activity is catalytically related to the HslVU protease.
  Biochemistry, 41, 7400-7406.  
12234933 J.Ortega, H.S.Lee, M.R.Maurizi, and A.C.Steven (2002).
Alternating translocation of protein substrates from both ends of ClpXP protease.
  EMBO J, 21, 4938-4949.  
12177439 J.R.Hoskins, K.Yanagihara, K.Mizuuchi, and S.Wickner (2002).
ClpAP and ClpXP degrade proteins with tags located in the interior of the primary sequence.
  Proc Natl Acad Sci U S A, 99, 11037-11042.  
12094726 O.Hlavácek, and L.Váchová (2002).
ATP-dependent proteinases in bacteria.
  Folia Microbiol (Praha), 47, 203-212.  
12032294 R.Ramachandran, C.Hartmann, H.K.Song, R.Huber, and M.Bochtler (2002).
Functional interactions of HslV (ClpQ) with the ATPase HslU (ClpY).
  Proc Natl Acad Sci U S A, 99, 7396-7401.  
12169602 S.Chiba, Y.Akiyama, and K.Ito (2002).
Membrane protein degradation by FtsH can be initiated from either end.
  J Bacteriol, 184, 4775-4782.  
12037319 S.Krzywda, A.M.Brzozowski, K.Karata, T.Ogura, and A.J.Wilkinson (2002).
Crystallization of the AAA domain of the ATP-dependent protease FtsH of Escherichia coli.
  Acta Crystallogr D Biol Crystallogr, 58, 1066-1067.  
11919638 T.Krojer, M.Garrido-Franco, R.Huber, M.Ehrmann, and T.Clausen (2002).
Crystal structure of DegP (HtrA) reveals a new protease-chaperone machine.
  Nature, 416, 455-459.
PDB code: 1ky9
12012346 V.Saridakis, D.Christendat, A.Thygesen, C.H.Arrowsmith, A.M.Edwards, and E.F.Pai (2002).
Crystal structure of Methanobacterium thermoautotrophicum conserved protein MTH1020 reveals an NTN-hydrolase fold.
  Proteins, 48, 141-143.
PDB code: 1kuu
11454203 D.Frees, P.Varmanen, and H.Ingmer (2001).
Inactivation of a gene that is highly conserved in Gram-positive bacteria stimulates degradation of non-native proteins and concomitantly increases stress tolerance in Lactococcus lactis.
  Mol Microbiol, 41, 93.  
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
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
11713188 M.R.Maurizi, and C.C.Li (2001).
AAA proteins: in search of a common molecular basis. International Meeting on Cellular Functions of AAA Proteins.
  EMBO Rep, 2, 980-985.  
11473577 T.Ogura, and A.J.Wilkinson (2001).
AAA+ superfamily ATPases: common structure--diverse function.
  Genes Cells, 6, 575-597.  
  11206054 C.Oinonen, and J.Rouvinen (2000).
Structural comparison of Ntn-hydrolases.
  Protein Sci, 9, 2329-2337.  
10809708 E.Krüger, E.Witt, S.Ohlmeier, R.Hanschke, and M.Hecker (2000).
The clp proteases of Bacillus subtilis are directly involved in degradation of misfolded proteins.
  J Bacteriol, 182, 3259-3265.  
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
10922051 J.R.Hoskins, S.K.Singh, M.R.Maurizi, and S.Wickner (2000).
Protein binding and unfolding by the chaperone ClpA and degradation by the protease ClpAP.
  Proc Natl Acad Sci U S A, 97, 8892-8897.  
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
10652097 M.N.Pouch, B.Cournoyer, and W.Baumeister (2000).
Characterization of the 20S proteasome from the actinomycete Frankia.
  Mol Microbiol, 35, 368-377.  
10500119 A.L.Horwich, E.U.Weber-Ban, and D.Finley (1999).
Chaperone rings in protein folding and degradation.
  Proc Natl Acad Sci U S A, 96, 11033-11040.  
10359771 C.K.Smith, T.A.Baker, and R.T.Sauer (1999).
Lon and Clp family proteases and chaperones share homologous substrate-recognition domains.
  Proc Natl Acad Sci U S A, 96, 6678-6682.  
10872471 D.Voges, P.Zwickl, and W.Baumeister (1999).
The 26S proteasome: a molecular machine designed for controlled proteolysis.
  Annu Rev Biochem, 68, 1015-1068.  
10359790 H.Stahlberg, E.Kutejová, K.Suda, B.Wolpensinger, A.Lustig, G.Schatz, A.Engel, and C.K.Suzuki (1999).
Mitochondrial Lon of Saccharomyces cerevisiae is a ring-shaped protease with seven flexible subunits.
  Proc Natl Acad Sci U S A, 96, 6787-6790.  
10320569 J.Porankiewicz, J.Wang, and A.K.Clarke (1999).
New insights into the ATP-dependent Clp protease: Escherichia coli and beyond.
  Mol Microbiol, 32, 449-458.  
10410804 M.Bochtler, L.Ditzel, M.Groll, C.Hartmann, and R.Huber (1999).
The proteasome.
  Annu Rev Biophys Biomol Struct, 28, 295-317.  
10508673 M.Schmidt, A.N.Lupas, and D.Finley (1999).
Structure and mechanism of ATP-dependent proteases.
  Curr Opin Chem Biol, 3, 584-591.  
10582236 P.Zwickl, D.Voges, and W.Baumeister (1999).
The proteasome: a macromolecular assembly designed for controlled proteolysis.
  Philos Trans R Soc Lond B Biol Sci, 354, 1501-1511.  
10081087 R.De Mot, I.Nagy, J.Walz, and W.Baumeister (1999).
Proteasomes and other self-compartmentalizing proteases in prokaryotes.
  Trends Microbiol, 7, 88-92.  
  10368141 W.F.Wu, Y.Zhou, and S.Gottesman (1999).
Redundant in vivo proteolytic activities of Escherichia coli Lon and the ClpYQ (HslUV) protease.
  J Bacteriol, 181, 3681-3687.  
10411632 Y.Li, J.Chen, W.Jiang, X.Mao, G.Zhao, and E.Wang (1999).
In vivo post-translational processing and subunit reconstitution of cephalosporin acylase from Pseudomonas sp. 130.
  Eur J Biochem, 262, 713-719.  
9666335 A.G.Murzin (1998).
How far divergent evolution goes in proteins.
  Curr Opin Struct Biol, 8, 380-387.  
9845366 N.Tamura, F.Lottspeich, W.Baumeister, and T.Tamura (1998).
The role of tricorn protease and its aminopeptidase-interacting factors in cellular protein degradation.
  Cell, 95, 637-648.  
9755166 U.Jenal, and T.Fuchs (1998).
An essential protease involved in bacterial cell-cycle control.
  EMBO J, 17, 5658-5669.  
9476896 W.Baumeister, J.Walz, F.Zühl, and E.Seemüller (1998).
The proteasome: paradigm of a self-compartmentalizing protease.
  Cell, 92, 367-380.  
9390550 C.N.Larsen, and D.Finley (1997).
Protein translocation channels in the proteasome and other proteases.
  Cell, 91, 431-434.  
9428517 I.Levchenko, C.K.Smith, N.P.Walsh, R.T.Sauer, and T.A.Baker (1997).
PDZ-like domains mediate binding specificity in the Clp/Hsp100 family of chaperones and protease regulatory subunits.
  Cell, 91, 939-947.  
9390554 J.Wang, J.A.Hartling, and J.M.Flanagan (1997).
The structure of ClpP at 2.3 A resolution suggests a model for ATP-dependent proteolysis.
  Cell, 91, 447-456.
PDB code: 1tyf
9390551 S.Gottesman, M.R.Maurizi, and S.Wickner (1997).
Regulatory subunits of energy-dependent proteases.
  Cell, 91, 435-438.  
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 code is shown on the right.

 

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