5YVT

Crystal structure of the alpha gamma heterodimer of human IDH3 in complex with Mg(2+) and NADH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.211 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Insights into the inhibitory mechanisms of NADH on the alpha gamma heterodimer of human NAD-dependent isocitrate dehydrogenase.

Liu, Y.Hu, L.Ma, T.Yang, J.Ding, J.

(2018) Sci Rep 8: 3146-3146

  • DOI: 10.1038/s41598-018-21584-7

  • PubMed Abstract: 
  • Human NAD-dependent isocitrate dehydrogenase (NAD-IDH) catalyzes the oxidative decarboxylation of isocitrate in the citric acid cycle. In the α <sub>2 </sub>βγ heterotetramer of NAD-IDH, the γ subunit plays the regulatory role and the β subunit the s ...

    Human NAD-dependent isocitrate dehydrogenase (NAD-IDH) catalyzes the oxidative decarboxylation of isocitrate in the citric acid cycle. In the α 2 βγ heterotetramer of NAD-IDH, the γ subunit plays the regulatory role and the β subunit the structural role. Previous biochemical data have shown that mammalian NAD-IDHs can be inhibited by NADH; however, the molecular mechanism is unclear. In this work, we show that the αβ, αγ and α 2 βγ enzymes of human NAD-IDH can be inhibited by NADH, and further determine the crystal structure of the αγ heterodimer bound with an Mg 2+ and an NADH at the active site and an NADH at the allosteric site, which resembles that of the inactive α Mg γ heterodimer. The NADH at the active site occupies the binding site for NAD + and prevents the binding of the cofactor. The NADH at the allosteric site occupies the binding sites for ADP and citrate and blocks the binding of the activators. The biochemical data confirm that the NADH binding competes with the binding of NAD + and the binding of citrate and ADP, and the two effects together contribute to the NADH inhibition on the activity. These findings provide insights into the inhibitory mechanisms of the αγ heterodimer by NADH.


    Organizational Affiliation

    School of Life Sciences, Shanghai University, 333 Nanchen Road, Shanghai, 200444, China.,State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China.,State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China. jpding@sibcb.ac.cn.,School of Life Science and Technology, ShanghaiTech University, 393 Hua-Xia Zhong Road, Shanghai, 201210, China. jpding@sibcb.ac.cn.




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): 0 
Gene Names: IDH3G
Find proteins for P51553 (Homo sapiens)
Go to Gene View: IDH3G
Go to UniProtKB:  P51553
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NAI
Query on NAI

Download SDF File 
Download CCD File 
A, B
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
NADH
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.211 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 118.027α = 90.00
b = 118.027β = 90.00
c = 142.109γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-11-27 
  • Released Date: 2018-03-14 
  • Deposition Author(s): Ma, T., Ding, J.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31230017
National Natural Science Foundation of ChinaChina31521061
Chinese Academy of SciencesChinaXDB08010302

Revision History 

  • Version 1.0: 2018-03-14
    Type: Initial release
  • Version 1.1: 2018-03-28
    Type: Database references