3BLW

Yeast Isocitrate Dehydrogenase with Citrate and AMP Bound in the Regulatory Subunits

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.3 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.274 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Allosteric Motions in Structures of Yeast NAD+-specific Isocitrate Dehydrogenase.

Hu, G., Hart, P.J., McAlister-Henn, L., Taylor, A.B.

(2008) J.Biol.Chem. 283: 10872-10880

  • DOI: 10.1074/jbc.M708719200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Mitochondrial NAD(+)-specific isocitrate dehydrogenases (IDHs) are key regulators of flux through biosynthetic and oxidative pathways in response to cellular energy levels. Here we present the first structures of a eukaryotic member of this enzyme fa ...

    Mitochondrial NAD(+)-specific isocitrate dehydrogenases (IDHs) are key regulators of flux through biosynthetic and oxidative pathways in response to cellular energy levels. Here we present the first structures of a eukaryotic member of this enzyme family, the allosteric, hetero-octameric, NAD(+)-specific IDH from yeast in three forms: 1) without ligands, 2) with bound analog citrate, and 3) with bound citrate + AMP. The structures reveal the molecular basis for ligand binding to homologous but distinct regulatory and catalytic sites positioned at the interfaces between IDH1 and IDH2 subunits and define pathways of communication between heterodimers and heterotetramers in the hetero-octamer. Disulfide bonds observed at the heterotetrameric interfaces in the unliganded IDH hetero-octamer are reduced in the ligand-bound forms, suggesting a redox regulatory mechanism that may be analogous to the "on-off" regulation of non-allosteric bacterial IDHs via phosphorylation. The results strongly suggest that eukaryotic IDH enzymes are exquisitely tuned to ensure that allosteric activation occurs only when concentrations of isocitrate are elevated.

    Organizational Affiliation: 

    Department of Biochemistry and X-ray Crystallography Core Laboratory, The University of Texas Health Science Center, San Antonio, Texas 78229, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Isocitrate dehydrogenase [NAD] subunit 1
A, C, E, G, I, K, M, O
349Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: IDH1
EC: 1.1.1.41
Find proteins for P28834 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: IDH1
Go to UniProtKB:  P28834
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Isocitrate dehydrogenase [NAD] subunit 2
B, D, F, H, J, L, N, P
354Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: IDH2
EC: 1.1.1.41
Find proteins for P28241 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: IDH2
Go to UniProtKB:  P28241
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP
Download SDF File 
Download CCD File 
A, C, E, G, I, K, M, O
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
FLC
Query on FLC
Download SDF File 
Download CCD File 
A, C, E, G, I, K, M, O
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.3 Å
  • R-Value Free: 0.311 
  • R-Value Work: 0.274 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 113.157α = 98.96
b = 116.346β = 110.23
c = 163.620γ = 106.63
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance