1AI2

ISOCITRATE DEHYDROGENASE COMPLEXED WITH ISOCITRATE, NADP+, AND CALCIUM (FLASH-COOLED)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Orbital steering in the catalytic power of enzymes: small structural changes with large catalytic consequences.

Mesecar, A.D.Stoddard, B.L.Koshland Jr., D.E.

(1997) Science 277: 202-206

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Small structural perturbations in the enzyme isocitrate dehydrogenase (IDH) were made in order to evaluate the contribution of precise substrate alignment to the catalytic power of an enzyme. The reaction trajectory of IDH was modified (i) after the ...

    Small structural perturbations in the enzyme isocitrate dehydrogenase (IDH) were made in order to evaluate the contribution of precise substrate alignment to the catalytic power of an enzyme. The reaction trajectory of IDH was modified (i) after the adenine moiety of nicotinamide adenine dinucleotide phosphate was changed to hypoxanthine (the 6-amino was changed to 6-hydroxyl), and (ii) by replacing Mg2+, which has six coordinating ligands, with Ca2+, which has eight coordinating ligands. Both changes make large (10(-3) to 10(-5)) changes in the reaction velocity but only small changes in the orientation of the substrates (both distance and angle) as revealed by cryocrystallographic trapping of active IDH complexes. The results provide evidence that orbital overlap produced by optimal orientation of reacting orbitals plays a major quantitative role in the catalytic power of enzymes.


    Related Citations: 
    • Structure of Isocitrate Dehydrogenase with Isocitrate, Nicotinamide Adenine Dinucleotide Phosphate, and Calcium at 2.5-A Resolution: A Pseudo-Michaelis Ternary Complex
      Stoddard, B.L.,Dean, A.,Koshland Junior, D.E.
      (1993) Biochemistry 32: 9310
    • Determinants of Cofactor Specificity in Isocitrate Dehydrogenase: Structure of an Engineered Nadp+--> Nad+ Specificity-Reversal Mutant
      Hurley, J.H.,Chen, R.,Dean, A.M.
      (1996) Biochemistry 35: 5670


    Organizational Affiliation

    Department of Molecular and Cell Biology, Stanley Hall, University of California, Berkeley, CA 94720, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ISOCITRATE DEHYDROGENASE
A
416Escherichia coli (strain K12)Mutation(s): 0 
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 2 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
ICA
Query on ICA

Download SDF File 
Download CCD File 
A
ISOCITRATE CALCIUM COMPLEX
C6 H7 Ca O7
AHEGTOWQUJMCIO-MASXSRPFDD
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NAPKi: 2700 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.191 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 102.300α = 90.00
b = 102.300β = 90.00
c = 150.500γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
X-PLORrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-10-15
    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