1SJS

ACCESS TO PHOSPHORYLATION IN ISOCITRATE DEHYDROGENASE MAY OCCUR BY DOMAIN SHIFTING


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Access to phosphorylation in isocitrate dehydrogenase may occur by domain shifting.

Finer-Moore, J.Tsutakawa, S.E.Cherbavaz, D.R.LaPorte, D.C.Koshland Jr., D.E.Stroud, R.M.

(1997) Biochemistry 36: 13890-13896

  • DOI: 10.1021/bi9711691

  • PubMed Abstract: 
  • To clarify further the mechanism of regulation by phosphorylation of isocitrate dehydrogenase, cocrystallization of isocitrate dehydrogenase and isocitrate dehydrogenase kinase/phosphatase in the presence of an ATP analog was attempted. Although cocr ...

    To clarify further the mechanism of regulation by phosphorylation of isocitrate dehydrogenase, cocrystallization of isocitrate dehydrogenase and isocitrate dehydrogenase kinase/phosphatase in the presence of an ATP analog was attempted. Although cocrystallization was unsuccessful, a new crystal form of isocitrate dehydrogenase was obtained which provides insight into the phosphorylation mechanism. The new, orthorhombic crystal form of isocitrate dehydrogenase is related to the previously reported tetragonal form largely by an approximately 16 degrees shift of a large domain relative to the small domain and clasp region within each subunit of the dimeric enzyme. The NADP+ cofactor binding surface is significantly disrupted by the shift to the open conformation. The solvent-accessible surface area and surface-enclosed volume increase by 2% relative to the dimeric tetragonal form. Most of the increase results from expansion of the active site cleft such that the distance across its opening increases from approximately 5 to 13 A, significantly increasing accessibility to Ser-113. The conformation of isocitrate dehydrogenase in the orthorhombic crystal form more closely resembles that of the crystal structure of the homologous enzyme 3-isopropylmalate dehydrogenase than does the tetragonal isocitrate dehydrogenase conformation. Since the crystal lattice forces are fairly weak, it appears that isocitrate dehydrogenase is a flexible molecule that can easily undergo domain shifts and possibly other induced fit conformational changes, to accommodate binding to isocitrate dehydrogenase kinase/phosphatase.


    Related Citations: 
    • 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 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
    • 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


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448, 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.181 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 124.500α = 90.00
b = 77.500β = 90.00
c = 92.100γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-12-03
    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