1Q3Q

Crystal structure of the chaperonin from Thermococcus strain KS-1 (two-point mutant complexed with AMP-PNP)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

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.

Shomura, Y., Yoshida, T., Iizuka, R., Maruyama, T., Yohda, M., Miki, K.

(2004) J.Mol.Biol. 335: 1265-1278

  • Primary Citation of Related Structures:  

  • PubMed 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 ac ...

    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.

    Related Citations: 
    • Crystallization and preliminary X-ray characterization of archaeal group II chaperonin alpha-subunit from Thermococcus strain KS-1
      Shomura, Y.,Yoshida, T.,Maruyama, T.,Yohda, M.,Miki, K.
      (2002) Acta Crystallogr.,Sect.D 58: 1830

    Organizational Affiliation: 

    Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thermosome alpha subunit
A, B, C, D
548Thermococcus sp. (strain JCM 11816 / KS-1)Mutation(s): 2 
Gene Names: thsA
Find proteins for P61112 (Thermococcus sp. (strain JCM 11816 / KS-1))
Go to UniProtKB:  P61112
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ANP
Query on ANP
Download SDF File 
Download CCD File 
A, B, C, D
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG
Download SDF File 
Download CCD File 
A, B, C, D
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.213 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 210.829α = 90.00
b = 210.829β = 90.00
c = 156.421γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
AMoREphasing
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-01-27
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Source and taxonomy, Version format compliance