5GRF

Crystal structure of the alpha gamma mutant (gamma-K151A) of human IDH3 in complex with Mg(2+), citrate and ADP

  • Classification: OXIDOREDUCTASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli BL21(DE3)
  • Mutation(s): 

  • Deposited: 2016-08-11 Released: 2017-02-15 
  • Deposition Author(s): Ma, T., Ding, J.
  • Funding Organization(s): the National Natural Science Foundation of China; the Ministry of Science and Technology of China; the Chinese Academy of Sciences 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Molecular mechanism of the allosteric regulation of the alpha gamma heterodimer of human NAD-dependent isocitrate dehydrogenase.

Ma, T.Peng, Y.Huang, W.Ding, J.

(2017) Sci Rep 7: 40921-40921

  • DOI: 10.1038/srep40921
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human NAD-dependent isocitrate dehydrogenase catalyzes the decarboxylation of isocitrate (ICT) into α-ketoglutarate in the Krebs cycle. It exists as the α <sub>2 </sub>βγ heterotetramer composed of the αβ and αγ heterodimers. Previously, we have demo ...

    Human NAD-dependent isocitrate dehydrogenase catalyzes the decarboxylation of isocitrate (ICT) into α-ketoglutarate in the Krebs cycle. It exists as the α 2 βγ heterotetramer composed of the αβ and αγ heterodimers. Previously, we have demonstrated biochemically that the α 2 βγ heterotetramer and αγ heterodimer can be allosterically activated by citrate (CIT) and ADP. In this work, we report the crystal structures of the αγ heterodimer with the γ subunit bound without or with different activators. Structural analyses show that CIT, ADP and Mg 2+ bind adjacent to each other at the allosteric site. The CIT binding induces conformational changes at the allosteric site, which are transmitted to the active site through the heterodimer interface, leading to stabilization of the ICT binding at the active site and thus activation of the enzyme. The ADP binding induces no further conformational changes but enhances the CIT binding through Mg 2+ -mediated interactions, yielding a synergistic activation effect. ICT can also bind to the CIT-binding subsite, which induces similar conformational changes but exhibits a weaker activation effect. The functional roles of the key residues are verified by mutagenesis, kinetic and structural studies. Our structural and functional data together reveal the molecular mechanism of the allosteric regulation of the αγ heterodimer.


    Organizational Affiliation

    Collaborative Innovation Center for Genetics and Development, Fudan University, 2005 Songhu Road, Shanghai 200438, China.,National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China.,Shanghai Science Research Center, Chinese Academy of Sciences, 333 Haike Road, Shanghai 201210, China.,School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial
A
339Homo sapiensMutation(s): 0 
Gene Names: IDH3A
EC: 1.1.1.41
Find proteins for P50213 (Homo sapiens)
Go to Gene View: IDH3A
Go to UniProtKB:  P50213
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial
B
354Homo sapiensMutation(s): 1 
Gene Names: IDH3G
Find proteins for P51553 (Homo sapiens)
Go to Gene View: IDH3G
Go to UniProtKB:  P51553
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
B
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
ADP
Query on ADP

Download SDF File 
Download CCD File 
B
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.207 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 114.336α = 90.00
b = 114.336β = 90.00
c = 143.901γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-08-11 
  • Released Date: 2017-02-15 
  • Deposition Author(s): Ma, T., Ding, J.

Funding OrganizationLocationGrant Number
the National Natural Science Foundation of ChinaChina31170690
the Ministry of Science and Technology of ChinaChina2011CB911102
the Chinese Academy of SciencesChinaXDB08010302

Revision History 

  • Version 1.0: 2017-02-15
    Type: Initial release
  • Version 1.1: 2017-10-04
    Type: Data collection