6SMN

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.125 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

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: 10.1038/s41598-019-56043-4
  • Primary Citation of Related Structures:  

  • 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) uni ...

    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

    Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia-Fondazione Cenci Bolognetti, P.le Aldo Moro 5, 00185, Roma, Italy.,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland. mruszkowski@ibch.poznan.pl.,Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, IL, USA. mruszkowski@ibch.poznan.pl.,Synchrotron Radiation Research Section of MCL, National Cancer Institute, Argonne, IL, USA.,Research Institute of Terrestrial Ecosystems, Italian National Research Council, Via Salaria Km. 29, 300-00015, Monterotondo Scalo, Roma, Italy.,Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA.,Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine hydroxymethyltransferase 2, mitochondrial
A, B, C
480Arabidopsis thalianaMutation(s): 0 
Gene Names: SHM2 (SHMT2)
EC: 2.1.2.1
Find proteins for Q94C74 (Arabidopsis thaliana)
Go to UniProtKB:  Q94C74
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Serine hydroxymethyltransferase 2, mitochondrial
D
480Arabidopsis thalianaMutation(s): 0 
Gene Names: SHM2 (SHMT2)
EC: 2.1.2.1
Find proteins for Q94C74 (Arabidopsis thaliana)
Go to UniProtKB:  Q94C74
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
SER
Query on SER

Download SDF File 
Download CCD File 
D
SERINE
C3 H7 N O3
MTCFGRXMJLQNBG-REOHCLBHSA-N
 Ligand Interaction
MTX
Query on MTX

Download SDF File 
Download CCD File 
A, B, C
METHOTREXATE
C20 H22 N8 O5
FBOZXECLQNJBKD-ZDUSSCGKSA-N
 Ligand Interaction
PLS
Query on PLS

Download SDF File 
Download CCD File 
A, B, C
[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE
PYRIDOXYL-SERINE-5-MONOPHOSPHATE
C11 H17 N2 O8 P
ODVKKQWXKRZJLG-VIFPVBQESA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
D
L-PEPTIDE LINKINGC14 H22 N3 O7 PLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.63 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.125 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 115.031α = 90.00
b = 130.401β = 90.00
c = 150.826γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-01-08
    Type: Initial release