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



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
  • Structures With Same Primary Citation

  • 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 ...

    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.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Serine hydroxymethyltransferase 2, mitochondrialA, B, C480Arabidopsis thalianaMutation(s): 0 
Gene Names: SHM2SHMT2At5g26780F2P16.40
EC: 2.1.2.1
Find proteins for Q94C74 (Arabidopsis thaliana)
Explore Q94C74 
Go to UniProtKB:  Q94C74
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Serine hydroxymethyltransferase 2, mitochondrialD480Arabidopsis thalianaMutation(s): 0 
Gene Names: SHM2SHMT2At5g26780F2P16.40
EC: 2.1.2.1
Find proteins for Q94C74 (Arabidopsis thaliana)
Explore Q94C74 
Go to UniProtKB:  Q94C74
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MTX
Query on MTX

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

Download CCD File 
A, B, C
[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL]-SERINE
C11 H17 N2 O8 P
ODVKKQWXKRZJLG-VIFPVBQESA-N
 Ligand Interaction
SER
Query on SER

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

Download CCD File 
A, B, C, D
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LLP
Query on LLP
DL-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
b = 130.401β = 90
c = 150.826γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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