1GRP

REGULATORY AND CATALYTIC MECHANISMS IN ESCHERICHIA COLI ISOCITRATE DEHYDROGENASE: MULTIPLE ROLES FOR N115


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Second-site suppression of regulatory phosphorylation in Escherichia coli isocitrate dehydrogenase.

Chen, R.Grobler, J.A.Hurley, J.H.Dean, A.M.

(1996) Protein Sci 5: 287-295

  • DOI: 10.1002/pro.5560050213
  • Primary Citation of Related Structures:  
    1GRP, 1GRO

  • PubMed Abstract: 
  • Inactivation of Escherichia coli isocitrate dehydrogenase upon phosphorylation at S113 depends upon the direct electrostatic repulsion of the negatively charged gamma-carboxylate of isocitrate by the negatively charged phosphoserine. The effect is mimicked by replacing S113 with aspartate or glutamate, which reduce performance (kcat/K(i) ...

    Inactivation of Escherichia coli isocitrate dehydrogenase upon phosphorylation at S113 depends upon the direct electrostatic repulsion of the negatively charged gamma-carboxylate of isocitrate by the negatively charged phosphoserine. The effect is mimicked by replacing S113 with aspartate or glutamate, which reduce performance (kcat/K(i).isocitrat/ Km.NADP) by a factor of 10(7). Here, we demonstrate that the inactivating effects of the electrostatic repulsion are completely eliminated by a second-site mutation, and provide the structural basis for this striking example of intragenic suppression. N115 is adjacent to S113 on one face of the D-helix, interacts with isocitrate and NADP+, and has been postulated to serve in both substrate binding and in catalysis. The single N115L substitution reduces affinity for isocitrate by a factor of 50 and performance by a factor of 500. However, the N115L substitution completely suppresses the inactivating electrostatic effects of S113D or S113E: the performance of the double mutants is 10(5) higher than the S113D and S113E single mutants. These mutations have little effect on the kinetics of alternative substrates, which lack the charged gamma-carboxylate of isocitrate. Both glutamate and aspartate at site 113 remain fully ionized in the presence of leucine. In the crystal structure of the N115L mutant, the leucine adopts a different conformer from the wild-type asparagine. Repacking around the leucine forces the amino-terminus of the D-helix away from the rest of the active site. The hydrogen bond between E113 and N115 in the S113E single mutant is broken in the S113E/N115L mutant, allowing the glutamate side chain to move away from the gamma-carboxylate of isocitrate. These movements increase the distance between the carboxylates, diminish the electrostatic repulsion, and lead to the remarkably high activity of the S113E/N115L mutant.


    Related Citations: 
    • 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

    Department of Biological Chemistry, Chicago Medical School, Illinois 60064-3095, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ISOCITRATE DEHYDROGENASEA416Escherichia coliMutation(s): 1 
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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ICTKi:  189000   nM  Binding MOAD
ICTKi :  189000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.195 
  • R-Value Observed: 0.195 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.1α = 90
b = 105.1β = 90
c = 150.6γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-04-03
    Type: Initial release
  • Version 1.1: 2008-03-24
    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