5X69

Human thymidylate synthase with a fragment bound in the dimer interface

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 

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:  
    5X5D, 5X4Y, 5X5A, 5X4X, 5X4W, 5X66, 5X67, 5X69, 5X5Q

  • PubMed Abstract: 

    • 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, ...

    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 Department of Medical Biochemistry & Biophysics, Division of Biophysics, Karolinska Institutet, Scheeles väg 2, Stockholm 17177, Sweden.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thymidylate synthase A, B, C, D, E, F290Homo sapiensMutation(s): 0 
Gene Names: TYMS, TS, OK/SW-cl.29
EC: 2.1.1.45
Find proteins for P04818 (Homo sapiens)
Explore P04818 
Go to UniProtKB:  P04818
NIH Common Fund Data Resources
PHAROS:  P04818
GTEx:  ENSG00000176890
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UMP
Query on UMP
Download Ideal Coordinates CCD File 
A, B, D, F
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N		 Ligand Interaction
7ZC
Query on 7ZC
Download Ideal Coordinates CCD File 
A, E
1-(5-methoxy-1H-indol-3-yl)-N,N-dimethyl-methanamine
C12 H16 N2 O
GOERTRUXQHDLHC-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.69 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.211 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.353α = 90
b = 109.353β = 90
c = 315.38γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data processing
PHASERphasing

Structure Validation

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View more in-depth experimental data

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
    Changes: Database references