7ZLW | pdb_00007zlw

NME1 in complex with ADP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.220 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.171 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 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 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.

Macromolecule Content 

  • Total Structure Weight: 107.5 kDa 
  • Atom Count: 7,745 
  • Modeled Residue Count: 895 
  • Deposited Residue Count: 936 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Nucleoside diphosphate kinase A
A, B, C, D, E
A, B, C, D, E, F
156Mus musculusMutation(s): 0 
Gene Names: Nme1Nm23
EC: 2.7.4.6 (PDB Primary Data), 3.1.24 (UniProt), 2.7.4.18 (UniProt), 2.7.11.1 (UniProt), 2.7.13.3 (UniProt), 3.1.11 (UniProt)
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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.220 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.171 (Depositor), 0.172 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.656α = 90
b = 70.193β = 90.96
c = 113.167γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
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
  • Version 1.2: 2024-10-16
    Changes: Structure summary
  • Version 1.3: 2026-03-04
    Changes: Refinement description