8ICD

REGULATION OF AN ENZYME BY PHOSPHORYLATION AT THE ACTIVE SITE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Regulation of an enzyme by phosphorylation at the active site.

Hurley, J.H.Dean, A.M.Sohl, J.L.Koshland, D.E.Stroud, R.M.

(1990) Science 249: 1012-1016

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The isocitrate dehydrogenase of Escherichia coli is an example of a ubiquitous class of enzymes that are regulated by covalent modification. In the three-dimensional structure of the enzyme-substrate complex, isocitrate forms a hydrogen bond with Ser ...

    The isocitrate dehydrogenase of Escherichia coli is an example of a ubiquitous class of enzymes that are regulated by covalent modification. In the three-dimensional structure of the enzyme-substrate complex, isocitrate forms a hydrogen bond with Ser113, the site of regulatory phosphorylation. The structures of Asp113 and Glu113 mutants, which mimic the inactivation of the enzyme by phosphorylation, show minimal conformational changes from wild type, as in the phosphorylated enzyme. Calculations based on observed structures suggest that the change in electrostatic potential when a negative charge is introduced either by phosporylation or site-directed mutagenesis is sufficient to inactivate the enzyme. Thus, direct interaction at a ligand binding site is an alternative mechanism to induced conformational changes from an allosteric site in the regulation of protein activity by phosphorylation.


    Related Citations: 
    • Structure of a Bacterial Enzyme Regulated by Phosphorylation, Isocitrate Dehydrogenase
      Hurley, J.H.,Thorsness, P.E.,Ramalingam, V.,Helmers, N.H.,Koshlandjunior, 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.,Koshlandjunior, 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.,Koshlandjunior, D.E.,Stroud, R.M.
      (1990) Science 249: 1012


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448.




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
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: 0.168 
  • 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-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1991-10-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    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