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 

Starting Model: experimental
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This is version 1.2 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: https://doi.org/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. 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isocitrate dehydrogenase [NAD] subunit alpha, mitochondrial339Homo 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
GTEx:  ENSG00000166411 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50213
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Isocitrate dehydrogenase [NAD] subunit gamma, mitochondrial354Homo 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
GTEx:  ENSG00000067829 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51553
Sequence Annotations
Expand
  • Reference Sequence
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

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description