9AYI | pdb_00009ayi

Human malic enzyme 2 cofactor complex at 1.89 Angstrom.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 
    0.201 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.178 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9AYI

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Interplay between malic enzyme 2, de novo serine synthesis, and the malate-aspartate shuttle drives metabolic adaptation in triple-negative breast cancer.

Jeon, J.H.Slayton, M.D.Krinkel, B.Animasahun, O.Shankaran, A.Wuchu, F.Nenwani, M.Farah, Z.Burke, J.Achreja, A.Nilaj, B.Kohagen, K.Eu, Y.H.Rosenfeld, A.Collard, M.Bao, L.Cheng, X.Kleer, C.Squire, C.Loomes, K.Nagrath, D.Merajver, S.D.

(2025) Cancer Metab 13: 42-42

  • DOI: https://doi.org/10.1186/s40170-025-00410-5
  • Primary Citation Related Structures: 
    9AYI, 9MYF

  • PubMed Abstract: 

    Triple-negative breast cancer (TNBC) is an aggressive and heterogeneous subtype of breast cancer with poor clinical outcomes. Malic enzyme 2 (ME2) is a mitochondrial enzyme that catalyzes the conversion of malate to pyruvate and has been proposed as a therapeutic target. ME2 is highly expressed in many cell types including TNBC cells. We sought to define the molecular and cellular consequences of ME2 inhibition to facilitate its clinical translation. Here, we systematically evaluated the cellular and molecular effects of ME2 knockdown (ME2kd) in multiple TNBC models. ME2kd had heterogeneous effects on proliferation, migration, and metabolic flexibility in TNBC cell lines. ME2kd MDA-MB-468 xenografts in nude mice grew significantly slower and conferred prolonged host survival. ME2kd caused distinct shifts in mitochondrial respiration and glycolysis, whereas metabolomic and transcriptomic analyses revealed altered tricarboxylic acid (TCA) cycle flux, glutamine consumption, and serine/glycine metabolism, partly through changes in malate-aspartate shuttle (MAS) activity. The interplay between ME2, the serine synthesis pathway and the MAS was investigated with metabolite deprivation and co-knockdown assays. Importantly, we determined the crystal structure of ME2 bound to the small-molecule inhibitor NPD-389 and identified the binding interactions that drive the inhibitory response. These findings help to clarify the role of ME2 in TNBC phenotypes and highlight the therapeutic potential of ME2 inhibition in precision oncology. [Image: see text] The online version contains supplementary material available at 10.1186/s40170-025-00410-5.


  • Organizational Affiliation
    • Department of Internal Medicine, Michigan Medicine, University of Michigan, Ann Arbor, MI, 48109, USA.

Macromolecule Content 

  • Total Structure Weight: 265.23 kDa 
  • Atom Count: 20,060 
  • Modeled Residue Count: 2,209 
  • Deposited Residue Count: 2,300 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NAD-dependent malic enzyme, mitochondrial
A, B, C, D
575Homo sapiensMutation(s): 0 
Gene Names: ME2
EC: 1.1.1.38
UniProt & NIH Common Fund Data Resources
Find proteins for P23368 (Homo sapiens)
Explore P23368 
Go to UniProtKB:  P23368
PHAROS:  P23368
GTEx:  ENSG00000082212 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23368
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD

Query on NAD



Download:Ideal Coordinates CCD File
AA [auth D]
E [auth A]
I [auth A]
M [auth B]
P [auth B]
AA [auth D],
E [auth A],
I [auth A],
M [auth B],
P [auth B],
U [auth C],
V [auth C],
Y [auth D]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
TLA

Query on TLA



Download:Ideal Coordinates CCD File
K [auth A],
N [auth B],
R [auth C],
W [auth D]
L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
O [auth B],
S [auth C],
Z [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
H [auth A],
L [auth B],
T [auth C],
X [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG

Query on MG



Download:Ideal Coordinates CCD File
J [auth A],
Q [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CSX
Query on CSX
A, B, C, D
L-PEPTIDE LINKINGC3 H7 N O3 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free:  0.201 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.177 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.178 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.325α = 65.32
b = 98.166β = 70.75
c = 107.739γ = 74.89
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release
  • Version 1.1: 2025-05-14
    Changes: Database references
  • Version 1.2: 2025-10-29
    Changes: Database references