2E5M

Crystal structure of isocitrate dehydrogenase from Sulfolobus tokodaii strain 7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.217 

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:  

  • 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 <i>Sulfolobus tokodaii </i> was isolated and crystallized. It shares high primary struc ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
409aa long hypothetical NADP-dependent isocitrate dehydrogenase
A, B
409Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)Mutation(s): 0 
Gene Names: idh (ST2166)
EC: 1.1.1.42
Find proteins for Q96YK6 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7))
Go to UniProtKB:  Q96YK6
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download SDF File 
Download CCD File 
A, B
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.217 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 74.780α = 90.00
b = 88.110β = 91.36
c = 75.670γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSphasing
ADSCdata collection
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-12-22 
  • Released Date: 2008-01-15 
  • Deposition Author(s): Kouyama, T., Kondo, H.

Revision History 

  • Version 1.0: 2008-01-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.2: 2019-01-23
    Type: Data collection, Database references
  • Version 1.3: 2020-01-01
    Type: Database references