2E5M | pdb_00002e5m

Crystal structure of isocitrate dehydrogenase from Sulfolobus tokodaii strain 7

• PDB DOI: https://doi.org/10.2210/pdb2E5M/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Sulfurisphaera tokodaii str. 7
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.279 (Depositor), 0.279 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.217 (Depositor) 

Starting Model: experimental

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

• PubMed: 30662370 
• DOI: https://doi.org/10.1155/2018/7571984
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Department of Physics, Graduate School of Science, Nagoya University, 464-8602 Nagoya, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 94.6 kDa 
• Atom Count: 6,947 
• Modeled Residue Count: 806 
• Deposited Residue Count: 818 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
409aa long hypothetical NADP-dependent isocitrate dehydrogenase	A, B	409	Sulfurisphaera tokodaii str. 7	Mutation(s): 0  EC: 1.1.1.42
UniProt
Find proteins for Q96YK6 (Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)) Explore Q96YK6  Go to UniProtKB:  Q96YK6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	C [auth A], D [auth B]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.279 (Depositor), 0.279 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.217 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.78	α = 90
b = 88.11	β = 91.36
c = 75.67	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• 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
  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
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description