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PDBsum entry 1q3q

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protein ligands metals Protein-protein interface(s) links
Chaperone PDB id
1q3q
Jmol
Contents
Protein chains
518 a.a. *
Ligands
ANP ×4
Metals
_MG ×4
Waters ×694
* Residue conservation analysis
PDB id:
1q3q
Name: Chaperone
Title: Crystal structure of the chaperonin from thermococcus strain (two-point mutant complexed with amp-pnp)
Structure: Thermosome alpha subunit. Chain: a, b, c, d. Synonym: thermosome subunit 1, chaperonin alpha subunit. Engineered: yes. Mutation: yes
Source: Thermococcus sp.. Organism_taxid: 79679. Strain: ks-1. Gene: thsa or cpka. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Biol. unit: Octamer (from PDB file)
Resolution:
2.30Å     R-factor:   0.213     R-free:   0.250
Authors: Y.Shomura,T.Yoshida,R.Iizuka,T.Maruyama,M.Yohda,K.Miki
Key ref:
Y.Shomura et al. (2004). Crystal structures of the group II chaperonin from Thermococcus strain KS-1: steric hindrance by the substituted amino acid, and inter-subunit rearrangement between two crystal forms. J Mol Biol, 335, 1265-1278. PubMed id: 14729342 DOI: 10.1016/j.jmb.2003.11.028
Date:
31-Jul-03     Release date:   27-Jan-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P61112  (THSA_THEK1) -  Thermosome subunit alpha
Seq:
Struc:
 
Seq:
Struc:
548 a.a.
518 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cellular protein metabolic process   2 terms 
  Biochemical function     nucleotide binding     3 terms  

 

 
DOI no: 10.1016/j.jmb.2003.11.028 J Mol Biol 335:1265-1278 (2004)
PubMed id: 14729342  
 
 
Crystal structures of the group II chaperonin from Thermococcus strain KS-1: steric hindrance by the substituted amino acid, and inter-subunit rearrangement between two crystal forms.
Y.Shomura, T.Yoshida, R.Iizuka, T.Maruyama, M.Yohda, K.Miki.
 
  ABSTRACT  
 
The crystal structures of the group II chaperonins consisting of the alpha subunit with amino acid substitutions of G65C and/or I125T from the hyperthermophilic archaeum Thermococcus strain KS-1 were determined. These mutants have been shown to be active in ATP hydrolysis but inactive in protein folding. The structures were shown to be double-ring hexadecamers in an extremely closed form, which was consistent with the crystal structure of native alpha8beta8-chaperonin from Thermoplasma acidophilum. Comparisons of the present structures with the atomic structures of the GroEL14-GroES7-(ADP)7 complex revealed that the deficiency in protein-folding activity with the G65C amino acid substitution is caused by the steric hindrance of the local conformational change in an equatorial domain. We concluded that this mutant chaperonin with G65C substitution is deprived of the smooth conformational change in the refolding-reaction cycle. We obtained a new form of crystal with a distinct space group at a lower concentration of sulfate ion in the presence of nucleotide. The crystal structure obtained at the lower concentration of sulfate ion tilts outward, and has much looser inter-subunit contacts compared with those in the presence of a higher concentration of sulfate ion. Such subunit rotation has never been characterized in group II chaperonins. The crystal structure obtained at the lower concentration of sulfate ion tilts outward, and has much looser inter-subunit contacts compared with those in the presence of a higher concentration of sulfate ion.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Structural comparisons between forms I and III. A, Superposition of a monomer model of form III (cyan) onto that of form I (light green). The models are drawn with a C^a model using MOLSCRIPT.[55.] The ADP-Mg molecule observed in the form III structure is indicated with a ball-and-stick model. B, An enlarged view of the protrusion with a C^a model using MOLSCRIPT.[55.] The directions of the a-helices H10 in both models are indicated with gray lines. C, D and E, Superposition of an octamer model of form I onto that of form III (C), of form I onto that of Ta a[8]b[8]-cpn (D), and of form III onto that of Ta a[8]b[8]-cpn (E). The models are pictured with the cylinder model. Subunit rearrangement between forms I and III can be represented by anti-clockwise rotation indicated with arrows in C.
Figure 4.
Figure 4. Comparisons of the form I structure with the GroEL[14]-ES[7]-(ADP)[7] structures. A, The superposition of a monomer structure of form I (cyan) with that of the cis-ring in GroEL[14]-ES[7]-(ADP)[7] complex (yellow). Apical domains are omitted from the models in A and B. B, The superposition of a monomer structure of form I (cyan) with that of the trans-ring in the GroEL[14]-ES[7]-(ADP)[7] complex (magenta). C, An enlarged stereo view of the area encompassed by the rectangle shown in B. The superposed models of form I (cyan), the cis-ring (yellow), and the trans-ring (magenta) are indicated. The transparent ball-and-stick model of the AMP-PNP molecule, which is refined in the AMP-PNP-bound form I, is shown as a reference. The arrows represent the direction of the putative residue displacement concomitant with the g-phosphate dissociation.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 335, 1265-1278) copyright 2004.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20885381 M.L.Baker, J.Zhang, S.J.Ludtke, and W.Chiu (2010).
Cryo-EM of macromolecular assemblies at near-atomic resolution.
  Nat Protoc, 5, 1697-1708.  
20471945 R.J.Tomko, M.Funakoshi, K.Schneider, J.Wang, and M.Hochstrasser (2010).
Heterohexameric ring arrangement of the eukaryotic proteasomal ATPases: implications for proteasome structure and assembly.
  Mol Cell, 38, 393-403.  
20173200 T.Kanzaki, S.Ushioku, A.Nakagawa, T.Oka, K.Takahashi, T.Nakamura, K.Kuwajima, A.Yamagishi, and M.Yohda (2010).
Adaptation of a hyperthermophilic group II chaperonin to relatively moderate temperatures.
  Protein Eng Des Sel, 23, 393-402.  
19229501 M.Sahlan, T.Kanzaki, and M.Yohda (2009).
Construction and characterization of the hetero-oligomer of the group II chaperonin from the hyperthermophilic archaeon, Thermococcus sp. strain KS-1.
  Extremophiles, 13, 437-445.  
18536725 C.R.Booth, A.S.Meyer, Y.Cong, M.Topf, A.Sali, S.J.Ludtke, W.Chiu, and J.Frydman (2008).
Mechanism of lid closure in the eukaryotic chaperonin TRiC/CCT.
  Nat Struct Mol Biol, 15, 746-753.  
17876827 E.Kurimoto, Y.Nishi, Y.Yamaguchi, T.Zako, R.Iizuka, N.Ide, M.Yohda, and K.Kato (2008).
Dynamics of group II chaperonin and prefoldin probed by 13C NMR spectroscopy.
  Proteins, 70, 1257-1263.  
18854314 T.Kanzaki, R.Iizuka, K.Takahashi, K.Maki, R.Masuda, M.Sahlan, H.Yébenes, J.M.Valpuesta, T.Oka, M.Furutani, N.Ishii, K.Kuwajima, and M.Yohda (2008).
Sequential action of ATP-dependent subunit conformational change and interaction between helical protrusions in the closure of the built-in lid of group II chaperonins.
  J Biol Chem, 283, 34773-34784.  
17440915 H.Y.Chen, Z.M.Chu, Y.H.Ma, Y.Zhang, and S.L.Yang (2007).
Expression and characterization of the chaperonin molecular machine from the hyperthermophilic archaeon Pyrococcus furiosus.
  J Basic Microbiol, 47, 132-137.  
17460696 S.Reissmann, C.Parnot, C.R.Booth, W.Chiu, and J.Frydman (2007).
Essential function of the built-in lid in the allosteric regulation of eukaryotic and archaeal chaperonins.
  Nat Struct Mol Biol, 14, 432-440.  
17072688 T.Yoshida, R.Iizuka, K.Itami, T.Yasunaga, H.Sakuraba, T.Ohshima, M.Yohda, and T.Maruyama (2007).
Comparative analysis of the protein folding activities of two chaperonin subunits of Thermococcus strain KS-1: the effects of beryllium fluoride.
  Extremophiles, 11, 225-235.  
16685467 T.Yoshida, T.Kanzaki, R.Iizuka, T.Komada, T.Zako, R.Suzuki, T.Maruyama, and M.Yohda (2006).
Contribution of the C-terminal region to the thermostability of the archaeal group II chaperonin from Thermococcus sp. strain KS-1.
  Extremophiles, 10, 451-459.  
15659368 M.Furutani, J.Hata, Y.Shomura, K.Itami, T.Yoshida, Y.Izumoto, A.Togi, A.Ideno, T.Yasunaga, K.Miki, and T.Maruyama (2005).
An engineered chaperonin caging a guest protein: Structural insights and potential as a protein expression tool.
  Protein Sci, 14, 341-350.  
15538645 M.Okochi, H.Matsuzaki, T.Nomura, N.Ishii, and M.Yohda (2005).
Molecular characterization of the group II chaperonin from the hyperthermophilic archaeum Pyrococcus horikoshii OT3.
  Extremophiles, 9, 127-134.  
16183634 R.Iizuka, T.Yoshida, N.Ishii, T.Zako, K.Takahashi, K.Maki, T.Inobe, K.Kuwajima, and M.Yohda (2005).
Characterization of archaeal group II chaperonin-ADP-metal fluoride complexes: implications that group II chaperonins operate as a "two-stroke engine".
  J Biol Chem, 280, 40375-40383.  
15145959 M.Okochi, T.Nomura, T.Zako, T.Arakawa, R.Iizuka, H.Ueda, T.Funatsu, M.Leroux, and M.Yohda (2004).
Kinetics and binding sites for interaction of the prefoldin with a group II chaperonin: contiguous non-native substrate and chaperonin binding sites in the archaeal prefoldin.
  J Biol Chem, 279, 31788-31795.  
14978026 R.Iizuka, S.So, T.Inobe, T.Yoshida, T.Zako, K.Kuwajima, and M.Yohda (2004).
Role of the helical protrusion in the conformational change and molecular chaperone activity of the archaeal group II chaperonin.
  J Biol Chem, 279, 18834-18839.  
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.