9CRA | pdb_00009cra

CryoEM Structure of the C-terminally truncated form of human NAD Kinase bound to NAD


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structure and regulation of human NAD kinase.

Praharaj, P.P.Li, Y.Mary, C.Soflaee, M.H.Ryu, K.Kim, D.Tran, D.H.Dey, T.Tom, H.J.Rion, H.Gelin, M.Lemoff, A.Zacharias, L.G.Patricio, J.S.Mathews, T.P.Chen, Z.Lionne, C.Hoxhaj, G.Labesse, G.

(2025) Sci Adv 11: eads2664-eads2664

  • DOI: https://doi.org/10.1126/sciadv.ads2664
  • Primary Citation of Related Structures:  
    9CR3, 9CR4, 9CRA

  • PubMed Abstract: 

    Reduced nicotinamide adenine dinucleotide phosphate (NADPH) is a crucial reducing cofactor for reductive biosynthesis and protection from oxidative stress. To fulfill their heightened anabolic and reductive power demands, cancer cells must boost their NADPH production. Progrowth and mitogenic protein kinases promote the activity of cytosolic NAD kinase (NADK), which produces NADP + , a limiting NADPH precursor. However, the molecular architecture and mechanistic regulation of human NADK remain undescribed. Here, we report the cryo-electron microscopy structure of human NADK, both in its apo-form and in complex with its substrate NAD + (nicotinamide adenine dinucleotide), revealing a tetrameric organization with distinct structural features. We discover that the amino (N)- and carboxyl (C)-terminal tails of NADK have opposing effects on its enzymatic activity and cellular NADP(H) levels. Specifically, the C-terminal region is critical for NADK activity, whereas the N-terminal region exhibits an inhibitory role. This study highlights molecular insights into the regulation of a vital enzyme governing NADP(H) production.


  • Organizational Affiliation

    Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NAD kinase
A, B, C, D
373Homo sapiensMutation(s): 0 
Gene Names: NADK
EC: 2.7.1.23
UniProt & NIH Common Fund Data Resources
Find proteins for O95544 (Homo sapiens)
Explore O95544 
Go to UniProtKB:  O95544
PHAROS:  O95544
GTEx:  ENSG00000008130 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95544
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.34 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
MODEL REFINEMENTCoot
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01GM143236
Welch FoundationUnited StatesI-2067-20210327
Welch FoundationUnited StatesI-2067-20240404
Agence Nationale de la Recherche (ANR)FranceANR-20-CE18-0025
Fondation pour la Recherche Medicale (FRM)FranceEQU202303016265

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-08
    Type: Initial release
  • Version 1.1: 2025-02-05
    Changes: Data collection, Database references
  • Version 1.2: 2025-02-12
    Changes: Data collection