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: 2.5 Å
  • R-Value Free: 0.271 
  • R-Value Work: 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.Mol.Biol. 5: 891-897

  • DOI: 10.1038/2331

  • 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: 
    • 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
    • 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 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.USA 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ISOCITRATE DEHYDROGENASE
A
414Escherichia coli (strain K12)Gene Names: icd (icdA, icdE)
EC: 1.1.1.42
Find proteins for P08200 (Escherichia coli (strain K12))
Go to UniProtKB:  P08200
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AKG
Query on AKG

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

Download SDF File 
Download CCD File 
A
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.222 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 106.100α = 90.00
b = 106.100β = 90.00
c = 151.800γ = 90.00
Software Package:
Software NamePurpose
LAUEGENdata reduction
X-PLORmodel building
LAUEGENdata scaling
X-PLORrefinement
X-PLORphasing
LAUEVIEWdata reduction
LAUEVIEWdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-05-04
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance