A. thaliana serine hydroxymethyltransferase isoform 2 (AtSHMT2) in complex with pemetrexed

Experimental Data Snapshot

  • Resolution: 1.54 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.129 

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Structural basis of methotrexate and pemetrexed action on serine hydroxymethyltransferases revealed using plant models.

Ruszkowski, M.Sekula, B.Ruszkowska, A.Contestabile, R.Nogues, I.Angelaccio, S.Szczepaniak, A.Dauter, Z.

(2019) Sci Rep 9: 19614-19614

  • DOI: https://doi.org/10.1038/s41598-019-56043-4
  • Primary Citation of Related Structures:  
    6SMN, 6SMR, 6SMW

  • PubMed Abstract: 

    Serine hydroxymethyltransferases (SHMTs) reversibly transform serine into glycine in a reaction accompanied with conversion of tetrahydrofolate (THF) into 5,10-methylene-THF (5,10-meTHF). In vivo, 5,10-meTHF is the main carrier of one-carbon (1C) units, which are utilized for nucleotide biosynthesis and other processes crucial for every living cell, but hyperactivated in overproliferating cells (e.g. cancer tissues). SHMTs are emerging as a promising target for development of new drugs because it appears possible to inhibit growth of cancer cells by cutting off the supply of 5,10-meTHF. Methotrexate (MTX) and pemetrexed (PTX) are two examples of antifolates that have cured many patients over the years but target different enzymes from the folate cycle (mainly dihydrofolate reductase and thymidylate synthase, respectively). Here we show crystal structures of MTX and PTX bound to plant SHMT isozymes from cytosol and mitochondria-human isozymes exist in the same subcellular compartments. We verify inhibition of the studied isozymes by a thorough kinetic analysis. We propose to further exploit antifolate scaffold in development of SHMT inhibitors because it seems likely that especially polyglutamylated PTX inhibits SHMTs in vivo. Structure-based optimization is expected to yield novel antifolates that could potentially be used as chemotherapeutics.

  • Organizational Affiliation

    Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, IL, USA. mruszkowski@ibch.poznan.pl.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine hydroxymethyltransferase 2, mitochondrial
A, B, C, D
480Arabidopsis thalianaMutation(s): 0 
Gene Names: SHM2SHMT2At5g26780F2P16.40
Find proteins for Q94C74 (Arabidopsis thaliana)
Explore Q94C74 
Go to UniProtKB:  Q94C74
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ94C74
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
LYA (Subject of Investigation/LOI)
Query on LYA

Download Ideal Coordinates CCD File 
GA [auth C],
N [auth A],
SA [auth D]
C20 H21 N5 O6
Query on PLS

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E [auth A],
P [auth B],
Z [auth C]
C11 H17 N2 O8 P
Query on PLP

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C8 H10 N O6 P
Query on SER

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C3 H7 N O3
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
CA [auth C]
DA [auth C]
EA [auth C]
AA [auth C],
BA [auth C],
CA [auth C],
DA [auth C],
EA [auth C],
F [auth A],
FA [auth C],
G [auth A],
H [auth A],
HA [auth C],
I [auth A],
IA [auth C],
J [auth A],
JA [auth C],
K [auth A],
KA [auth C],
L [auth A],
M [auth A],
MA [auth C],
NA [auth C],
O [auth A],
OA [auth D],
PA [auth D],
Q [auth B],
QA [auth D],
R [auth B],
RA [auth D],
S [auth B],
T [auth B],
TA [auth D],
U [auth B],
UA [auth D],
V [auth B],
VA [auth D],
W [auth B],
WA [auth D],
X [auth B],
Y [auth B]
C2 H6 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.54 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.129 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.899α = 90
b = 130.288β = 90
c = 150.777γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-08
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description