7ZL8

NME1 in complex with succinyl-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Nucleoside diphosphate kinases 1 and 2 regulate a protective liver response to a high-fat diet.

Iuso, D.Garcia-Saez, I.Coute, Y.Yamaryo-Botte, Y.Boeri Erba, E.Adrait, A.Zeaiter, N.Tokarska-Schlattner, M.Jilkova, Z.M.Boussouar, F.Barral, S.Signor, L.Couturier, K.Hajmirza, A.Chuffart, F.Bourova-Flin, E.Vitte, A.L.Bargier, L.Puthier, D.Decaens, T.Rousseaux, S.Botte, C.Schlattner, U.Petosa, C.Khochbin, S.

(2023) Sci Adv 9: eadh0140-eadh0140

  • DOI: https://doi.org/10.1126/sciadv.adh0140
  • Primary Citation of Related Structures:  
    7ZL8, 7ZLW, 7ZTK

  • PubMed Abstract: 

    The synthesis of fatty acids from acetyl-coenzyme A (AcCoA) is deregulated in diverse pathologies, including cancer. Here, we report that fatty acid accumulation is negatively regulated by nucleoside diphosphate kinases 1 and 2 (NME1/2), housekeeping enzymes involved in nucleotide homeostasis that were recently found to bind CoA. We show that NME1 additionally binds AcCoA and that ligand recognition involves a unique binding mode dependent on the CoA/AcCoA 3' phosphate. We report that Nme2 knockout mice fed a high-fat diet (HFD) exhibit excessive triglyceride synthesis and liver steatosis. In liver cells, NME2 mediates a gene transcriptional response to HFD leading to the repression of fatty acid accumulation and activation of a protective gene expression program via targeted histone acetylation. Our findings implicate NME1/2 in the epigenetic regulation of a protective liver response to HFD and suggest a potential role in controlling AcCoA usage between the competing paths of histone acetylation and fatty acid synthesis.


  • Organizational Affiliation

    Univ. Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences, La Tronche 38706, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoside diphosphate kinase A
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
156Mus musculusMutation(s): 0 
Gene Names: Nme1Nm23
EC: 2.7.4.6
UniProt
Find proteins for P15532 (Mus musculus)
Explore P15532 
Go to UniProtKB:  P15532
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15532
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SCA (Subject of Investigation/LOI)
Query on SCA

Download Ideal Coordinates CCD File 
M [auth A]
N [auth B]
O [auth C]
P [auth D]
Q [auth E]
M [auth A],
N [auth B],
O [auth C],
P [auth D],
Q [auth E],
R [auth F],
S [auth G],
T [auth H],
U [auth I],
V [auth J],
W [auth K],
X [auth L]
SUCCINYL-COENZYME A
C25 H40 N7 O19 P3 S
VNOYUJKHFWYWIR-ITIYDSSPSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.844α = 90
b = 69.087β = 89.72
c = 225.127γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2023-08-09
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references