1IDE

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 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

  • Primary Citation of Related Structures:  1IDC, 1IDD, 1IDF

  • 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
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ISOCITRATE DEHYDROGENASE
A
416Escherichia 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
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
ICT
Query on ICT

Download SDF File 
Download CCD File 
A
ISOCITRIC ACID
C6 H8 O7
ODBLHEXUDAPZAU-ZAFYKAAXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.192 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 105.100α = 90.00
b = 105.100β = 90.00
c = 150.300γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORphasing
OXFORDdata reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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