1IKA

STRUCTURE OF ISOCITRATE DEHYDROGENASE WITH ALPHA-KETOGLUTARATE AT 2.7 ANGSTROMS RESOLUTION: CONFORMATIONAL CHANGES INDUCED BY DECARBOXYLATION OF ISOCITRATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of isocitrate dehydrogenase with alpha-ketoglutarate at 2.7-A resolution: conformational changes induced by decarboxylation of isocitrate.

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

(1993) Biochemistry 32: 9317-9322

  • DOI: 10.1021/bi00087a009
  • Primary Citation of Related Structures:  
    1IKA

  • PubMed Abstract: 
  • The structure of the isocitrate dehydrogenase (IDH) complex with bound alpha-ketoglutarate, Ca2+, and NADPH was solved at 2.7-A resolution. The alpha-ketoglutarate binds in the active site at the same position and orientation as isocitrate, with a difference between the two bound molecules of about 0 ...

    The structure of the isocitrate dehydrogenase (IDH) complex with bound alpha-ketoglutarate, Ca2+, and NADPH was solved at 2.7-A resolution. The alpha-ketoglutarate binds in the active site at the same position and orientation as isocitrate, with a difference between the two bound molecules of about 0.8 A. The Ca2+ metal is coordinated by alpha-ketoglutarate, three conserved aspartate residues, and a pair of water molecules. The largest motion in the active site relative to the isocitrate enzyme complex is observed for tyrosine 160, which originally forms a hydrogen bond to the labile carboxyl group of isocitrate and moves to form a new hydrogen bond to Asp 307 in the complex with alpha-ketoglutarate. This triggers a number of significant movements among several short loops and adjoining secondary structural elements in the enzyme, most of which participate in dimer stabilization and formation of the active-site cleft. These rearrangements are similar to the ligand-binding-induced movements observed in globins and insulin and serve as a model for an enzymatic mechanism which involves local shifts of secondary structural elements during turnover, rather than large-scale domain closures or loop transitions induced by substrate binding such as those observed in hexokinase or triosephosphate isomerase.


    Related Citations: 
    • The Structure of Isocitrate Dehydrogenase with Isocitrate, Nadp, and Calcium at 2.5 Angstroms Resolution: A Pseudo-Michaelis Ternary Complex
      Stoddard, B.L., Dean, A., Koshland Junior, D.E.
      (1993) Biochemistry 32: 9310

    Organizational Affiliation

    Department of Molecular and Cellular Biology, University of California, Berkeley 94720.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ISOCITRATE DEHYDROGENASEA416Escherichia coliMutation(s): 0 
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
AKG
Query on AKG

Download CCD File 
A
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.1α = 90
b = 105.1β = 90
c = 150.3γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-07-31
    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: 2019-07-17
    Changes: Advisory, Data collection, Other, Refinement description
  • Version 1.4: 2019-08-14
    Changes: Data collection, Refinement description