2E0C

crystal structure of isocitrate dehydrogenase from Sulfolobus tokodaii strain7 at 2.0 A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Crystal Structures of the Putative Isocitrate Dehydrogenase fromSulfolobus tokodaiiStrain 7 in the Apo and NADP+-Bound Forms.

Kondo, H., Murakami, M.

(2018) Archaea 2018: 7571984-7571984

  • DOI: 10.1155/2018/7571984
  • Primary Citation of Related Structures:  
    2E0C, 2E5M

  • PubMed Abstract: 

    • Isocitrate dehydrogenase is a catabolic enzyme that acts during the third step of the tricarboxylic acid cycle. The hypothetical protein ST2166 from the archaeon Sulfolobus tokodaii was isolated and crystallized. It shares high primary structure homology with prokaryotic NADP + -dependent IDHs, suggesting that these enzymes share a common enzymatic mechanism ...

    Isocitrate dehydrogenase is a catabolic enzyme that acts during the third step of the tricarboxylic acid cycle. The hypothetical protein ST2166 from the archaeon Sulfolobus tokodaii was isolated and crystallized. It shares high primary structure homology with prokaryotic NADP + -dependent IDHs, suggesting that these enzymes share a common enzymatic mechanism. The crystal structure of ST2166 was determined at 2.0 Å resolution in the apo form, and then the structure of the crystal soaked with NADP + was also determined at 2.4 Å resolution, which contained NADP + bound at the putative active site. Comparisons between the structures of apo and NADP + -bound forms and NADP-IDHs from other prokaryotes suggest that prokaryotic NADP-IDHs recognize their cofactors using conserved Lys335, Tyr336, and Arg386 in ST2166 at the opening cleft before the domain closure.

    Organizational Affiliation: 

    Department of Physics, Graduate School of Science, Nagoya University, 464-8602 Nagoya, Japan.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
409aa long hypothetical NADP-dependent isocitrate dehydrogenaseA, B409Sulfurisphaera tokodaii str. 7Mutation(s): 0 
Gene Names: idh, ST2166, STK_21660
EC: 1.1.1.42
Find proteins for Q96YK6 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7))
Explore Q96YK6 
Go to UniProtKB:  Q96YK6
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.247 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.88α = 90
b = 87.72β = 91.37
c = 75.72γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
CNSphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2006-10-06 
  • Released Date: 2007-10-30 
    • Deposition Author(s): Kouyama, T.

Revision History  (Full details and data files)

  • Version 1.0: 2007-10-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2019-01-23
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Database references