8EYN

Crystal Structure of Human Mitochondrial NADP+ Malic Enzyme 3 in Apo Form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Integrative structural and functional analysis of human malic enzyme 3: A potential therapeutic target for pancreatic cancer.

Grell, T.A.J.Mason, M.Thompson, A.A.Gomez-Tamayo, J.C.Riley, D.Wagner, M.V.Steele, R.Ortiz-Meoz, R.F.Wadia, J.Shaffer, P.L.Tresadern, G.Sharma, S.Yu, X.

(2022) Heliyon 8: e12392-e12392

  • DOI: https://doi.org/10.1016/j.heliyon.2022.e12392
  • Primary Citation of Related Structures:  
    8E76, 8E78, 8E8O, 8EYN, 8EYO

  • PubMed Abstract: 

    Malic enzymes (ME1, ME2, and ME3) are involved in cellular energy regulation, redox homeostasis, and biosynthetic processes, through the production of pyruvate and reducing agent NAD(P)H. Recent studies have implicated the third and least well-characterized isoform, mitochondrial NADP + -dependent malic enzyme 3 (ME3), as a therapeutic target for pancreatic cancers. Here, we utilized an integrated structure approach to determine the structures of ME3 in various ligand-binding states at near-atomic resolutions. ME3 is captured in the open form existing as a stable tetramer and its dynamic Domain C is critical for activity. Catalytic assay results reveal that ME3 is a non-allosteric enzyme and does not require modulators for activity while structural analysis suggests that the inner stability of ME3 Domain A relative to ME2 disables allostery in ME3. With structural information available for all three malic enzymes, the foundation has been laid to understand the structural and biochemical differences of these enzymes and could aid in the development of specific malic enzyme small molecule drugs.


  • Organizational Affiliation

    Structural and Protein Sciences, Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NADP-dependent malic enzyme, mitochondrial
A, B
568Homo sapiensMutation(s): 0 
Gene Names: ME3
EC: 1.1.1.40
UniProt & NIH Common Fund Data Resources
Find proteins for Q16798 (Homo sapiens)
Explore Q16798 
Go to UniProtKB:  Q16798
PHAROS:  Q16798
GTEx:  ENSG00000151376 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16798
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.75α = 90
b = 75.13β = 90
c = 118.7γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2023-02-08
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description