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: 2.40 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

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
  • Primary Citation of Related Structures:  
    5YVT

  • PubMed Abstract: 
  • 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 ...

    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 Science and Technology, ShanghaiTech University, 393 Hua-Xia Zhong Road, Shanghai, 201210, China. jpding@sibcb.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrialA339Homo sapiensMutation(s): 0 
Gene Names: IDH3A
EC: 1.1.1.41
UniProt & NIH Common Fund Data Resources
Find proteins for P50213 (Homo sapiens)
Explore P50213 
Go to UniProtKB:  P50213
PHAROS:  P50213
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrialB354Homo sapiensMutation(s): 0 
Gene Names: IDH3G
UniProt & NIH Common Fund Data Resources
Find proteins for P51553 (Homo sapiens)
Explore P51553 
Go to UniProtKB:  P51553
PHAROS:  P51553
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAI
Query on NAI

Download Ideal Coordinates CCD File 
D [auth A], E [auth B]1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NAIKd:  109000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.027α = 90
b = 118.027β = 90
c = 142.109γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report



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  (Full details and data files)

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