1BL5

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


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 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: 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 us ...

    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.


    Related Citations: 
    • Catalytic Mechanism of Nadp(+)-Dependent Isocitrate Dehydrogenase: Implications from the Structures of Magnesium-Isocitrate and Nadp+ Complexes
      Hurley, J.H., Dean, A.M., Koshland Junior, D.E., Stroud, R.M.
      (1991) Biochemistry 30: 8671
    • Regulation of Isocitrate Dehydrogenase by Phosphorylation Involves No Long-Range Conformational Change in the Free Enzyme
      Hurley, J.H., Dean, A.M., Thorsness, P.E., Koshland Junior, D.E., Stroud, R.M.
      (1990) J Biol Chem 265: 3599
    • Regulation of an Enzyme by Phosphorylation at the Active Site
      Hurley, J.H., Dean, A.M., Sohl, J.L., Koshland Junior, D.E., Stroud, R.M.
      (1990) Science 249: 1012
    • Structure of a Bacterial Enzyme Regulated by Phosphorylation, Isocitrate Dehydrogenase
      Hurley, J.H., Thorsness, P.E., Ramalingam, V., Helmers, N.H., Koshland Junior, D.E., Stroud, R.M.
      (1989) Proc Natl Acad Sci U S A 86: 8635

    Organizational Affiliation

    Division of Basic Sciences, Program in Structural Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA. bstoddar@fred.fhcrc.org



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ISOCITRATE DEHYDROGENASEA414Escherichia coliMutation(s): 0 
Gene Names: icd
EC: 1.1.1.42
Find proteins for P08200 (Escherichia coli (strain K12))
Explore P08200 
Go to UniProtKB:  P08200
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
AKG
Query on AKG

Download CCD File 
A
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
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 = 106.1α = 90
b = 106.1β = 90
c = 151.8γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
LAUEVIEWdata reduction
LAUEGENdata reduction
LAUEVIEWdata scaling
LAUEGENdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

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