4KZO

Crystal Structure Analysis of human IDH1 mutants in complex with NADP+ and Ca2+/alpha-Ketoglutarate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.204 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Mutant IDH1 Enhances the Production of 2-Hydroxyglutarate Due to Its Kinetic Mechanism.

Rendina, A.R.Pietrak, B.Smallwood, A.Zhao, H.Qi, H.Quinn, C.Adams, N.D.Concha, N.Duraiswami, C.Thrall, S.H.Sweitzer, S.Schwartz, B.

(2013) Biochemistry 52: 4563-4577

  • DOI: 10.1021/bi400514k
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The human, cytosolic enzyme isocitrate dehydrogenase 1 (IDH1) reversibly converts isocitrate to α-ketoglutarate (αKG). Cancer-associated somatic mutations in IDH1 result in a loss of this normal function but a gain in a new or neomorphic ability to c ...

    The human, cytosolic enzyme isocitrate dehydrogenase 1 (IDH1) reversibly converts isocitrate to α-ketoglutarate (αKG). Cancer-associated somatic mutations in IDH1 result in a loss of this normal function but a gain in a new or neomorphic ability to convert αKG to the oncometabolite 2-hydroxyglutarate (2HG). To improve our understanding of the basis for this phenomenon, we have conducted a detailed kinetic study of wild-type IDH1 as well as the known 2HG-producing clinical R132H and G97D mutants and mechanistic Y139D and (newly described) G97N mutants. In the reductive direction of the normal reaction (αKG to isocitrate), dead-end inhibition studies suggest that wild-type IDH1 goes through a random sequential mechanism, similar to previous reports on related mammalian IDH enzymes. However, analogous experiments studying the reductive neomorphic reaction (αKG to 2HG) with the mutant forms of IDH1 are more consistent with an ordered sequential mechanism, with NADPH binding before αKG. This result was further confirmed by primary kinetic isotope effects for which saturating with αKG greatly reduced the observed isotope effect on (D)(V/K)NADPH. For the mutant IDH1 enzyme, the change in mechanism was consistently associated with reduced efficiencies in the use of αKG as a substrate and enhanced efficiencies using NADPH as a substrate. We propose that the sum of these kinetic changes allows the mutant IDH1 enzymes to reductively trap αKG directly into 2HG, rather than allowing it to react with carbon dioxide and form isocitrate, as occurs in the wild-type enzyme.


    Organizational Affiliation

    Departments of Biological Reagents and Assay Development, Cancer Epigenetics, and Computational and Structural Chemistry, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Isocitrate dehydrogenase [NADP] cytoplasmic
A, B, C
425Homo sapiensGene Names: IDH1 (PICD)
EC: 1.1.1.42
Find proteins for O75874 (Homo sapiens)
Go to Gene View: IDH1
Go to UniProtKB:  O75874
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AKG
Query on AKG

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Download CCD File 
A, B, C
2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N
 Ligand Interaction
NAP
Query on NAP

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Download CCD File 
A, B, C
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NAPKd: 43 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.204 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.178 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 96.360α = 90.00
b = 274.598β = 90.00
c = 115.990γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-07-17
    Type: Initial release