5X67

Human thymidylate synthase in complex with dUMP and nolatrexed


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.153 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural analyses of human thymidylate synthase reveal a site that may control conformational switching between active and inactive states.

Chen, D.Jansson, A.Sim, D.Larsson, A.Nordlund, P.

(2017) J. Biol. Chem. 292: 13449-13458

  • DOI: 10.1074/jbc.M117.787267
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Thymidylate synthase (TS) is the sole enzyme responsible for <i>de novo </i> biosynthesis of thymidylate (TMP) and is essential for cell proliferation and survival. Inhibition of human TS (hTS) has been extensively investigated for cancer chemothera ...

    Thymidylate synthase (TS) is the sole enzyme responsible for de novo biosynthesis of thymidylate (TMP) and is essential for cell proliferation and survival. Inhibition of human TS (hTS) has been extensively investigated for cancer chemotherapy, but several aspects of its activity and regulation are still uncertain. In this study, we performed comprehensive structural and biophysical studies of hTS using crystallography and thermal shift assay and provided the first detailed structural information on the conformational changes induced by ligand binding to the hTS active site. We found that upon binding of the antifolate agents raltitrexed and nolatrexed, the two insert regions in hTS, the functions of which are unclear, undergo positional shifts toward the catalytic center. We investigated the inactive conformation of hTS and found that the two insert regions are also involved in the conformational transition between the active and inactive state of hTS. Moreover, we identified a ligand-binding site in the dimer interface, suggesting that the cavity in the dimer interface could serve as an allosteric site of hTS to regulate the conformational switching between the active and inactive states. On the basis of these findings, we propose a regulatory mechanism of hTS activity that involves allosteric regulation of interactions of hTS with its own mRNA depending on cellular demands for TMP.


    Organizational Affiliation

    the Institute of Cellular and Molecular Biology, A*STAR, 61 Biopolis Drive (Proteos), Singapore 138673, and.,From the School of Biological Sciences, Lab 07-02 and andreas.larsson@ntu.edu.sg.,the Department of Medical Biochemistry & Biophysics, Division of Biophysics, Karolinska Institutet, Scheeles väg 2, Stockholm 17177, Sweden.,Lab 07-01, Nanyang Technological University, 61 Biopolis Drive (Proteos), Singapore 138673.,From the School of Biological Sciences, Lab 07-02 and PNORDLUND@ntu.edu.sg.,From the School of Biological Sciences, Lab 07-02 and.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidylate synthase
A, B
290Homo sapiensMutation(s): 0 
Gene Names: TYMS (TS)
EC: 2.1.1.45
Find proteins for P04818 (Homo sapiens)
Go to Gene View: TYMS
Go to UniProtKB:  P04818
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7Z9
Query on 7Z9

Download SDF File 
Download CCD File 
A, B
2-azanyl-6-methyl-5-pyridin-4-ylsulfanyl-3H-quinazolin-4-one
Nolatrexed, 2-Amino-6-methyl-5-(4-pyridylthio)-1H-quinazolin-4-one
C14 H12 N4 O S
XHWRWCSCBDLOLM-UHFFFAOYSA-N
 Ligand Interaction
UMP
Query on UMP

Download SDF File 
Download CCD File 
A, B
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
DUMP
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UMPKd: 1190 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.13 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.153 
  • Space Group: P 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 108.290α = 90.00
b = 108.290β = 90.00
c = 106.034γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata processing
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Nanyang Technological UniversitySingaporeM060080004.70301200

Revision History 

  • Version 1.0: 2017-06-28
    Type: Initial release
  • Version 1.1: 2017-08-30
    Type: Database references