1IDE

ISOCITRATE DEHYDROGENASE Y160F MUTANT STEADY-STATE INTERMEDIATE COMPLEX (LAUE DETERMINATION)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.192 
  • R-Value Observed: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Mutagenesis and Laue structures of enzyme intermediates: isocitrate dehydrogenase.

Bolduc, J.M.Dyer, D.H.Scott, W.G.Singer, P.Sweet, R.M.Koshland Jr., D.E.Stoddard, B.L.

(1995) Science 268: 1312-1318

  • DOI: 10.1126/science.7761851
  • Primary Citation of Related Structures:  
    1IDC, 1IDF, 1IDE, 1IDD

  • PubMed Abstract: 
  • Site-directed mutagenesis and Laue diffraction data to 2.5 A resolution were used to solve the structures of two sequential intermediates formed during the catalytic actions of isocitrate dehydrogenase. Both intermediates are distinct from the enzyme ...

    Site-directed mutagenesis and Laue diffraction data to 2.5 A resolution were used to solve the structures of two sequential intermediates formed during the catalytic actions of isocitrate dehydrogenase. Both intermediates are distinct from the enzyme-substrate and enzyme-product complexes. Mutation of key catalytic residues changed the rate determining steps so that protein and substrate intermediates within the overall reaction pathway could be visualized.


    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

    Fred Hutchinson Cancer Research Center, Program in Structural Biology, Seattle, WA 98104, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ISOCITRATE DEHYDROGENASEA416Escherichia coliMutation(s): 1 
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
ICT
Query on ICT

Download CCD File 
A
ISOCITRIC ACID
C6 H8 O7
ODBLHEXUDAPZAU-ZAFYKAAXSA-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 Work: 0.192 
  • R-Value Observed: 0.192 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.1α = 90
b = 105.1β = 90
c = 150.3γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
OXFORDdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-03-08
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other