1BL5

ISOCITRATE DEHYDROGENASE FROM E. COLI SINGLE TURNOVER LAUE STRUCTURE OF RATE-LIMITED PRODUCT COMPLEX, 10 MSEC TIME RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb1BL5/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-07-23 Released: 1999-05-04 
• Deposition Author(s): Stoddard, B.L., Cohen, B., Brubaker, M., Mesecar, A., Koshland Junior, D.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.271 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 

Literature

Millisecond Laue structures of an enzyme-product complex using photocaged substrate analogs.

Stoddard, B.L., Cohen, B.E., Brubaker, M., Mesecar, A.D., Koshland Jr., D.E.

(1998) Nat Struct Biol 5: 891-897

• PubMed: 9783749 
• DOI: https://doi.org/10.1038/2331
• Primary Citation of Related Structures:  
  1BL5


• PubMed Abstract: 
  

  The structure of a rate-limited product complex formed during a single initial round of turnover by isocitrate dehydrogenase has been determined. Photolytic liberation of either caged substrate or caged cofactor and Laue X-ray data collection were used to visualize the complex, which has a minimum half-life of approximately 10 milliseconds. The experiment was conducted with three different photoreactive compounds, each possessing a unique mechanism leading to the formation of the enzyme-substrate (ES) complex. Photoreaction efficiency and subsequent substrate affinities and binding rates in the crystal are critical parameters for these experiments. The structure suggests that CO2 dissociation is a rapid event that may help drive product formation, and that small conformational changes may contribute to slow product release.

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Organizational Affiliation: 

Division of Basic Sciences, Program in Structural Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA. [e-mail]

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: 46.46 kDa 
• Atom Count: 3,317 
• Modelled Residue Count: 414 
• Deposited Residue Count: 414 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ISOCITRATE DEHYDROGENASE	A	414	Escherichia coli	Mutation(s): 0  Gene Names: ICD EC: 1.1.1.42
UniProt
Find proteins for P08200 (Escherichia coli (strain K12)) Explore P08200  Go to UniProtKB:  P08200

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP	D [auth A]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
AKG	C [auth A]	2-OXOGLUTARIC ACID C5 H6 O5 KPGXRSRHYNQIFN-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.271 
• R-Value Work: 0.222 
• R-Value Observed: 0.222 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 106.1	α = 90
b = 106.1	β = 90
c = 151.8	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
LaueView	data reduction
LAUEGEN	data reduction
LaueView	data scaling
LAUEGEN	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-05-04 
Deposition Author(s): Stoddard, B.L., Cohen, B., Brubaker, M., Mesecar, A., Koshland Junior, D.E.

Revision History  

• Version 1.0: 1999-05-04
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description