3N5E

Crystal Structure of human thymidylate synthase bound to a peptide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Protein-protein interface-binding peptides inhibit the cancer therapy target human thymidylate synthase.

Cardinale, D.Guaitoli, G.Tondi, D.Luciani, R.Henrich, S.Salo-Ahen, O.M.Ferrari, S.Marverti, G.Guerrieri, D.Ligabue, A.Frassineti, C.Pozzi, C.Mangani, S.Fessas, D.Guerrini, R.Ponterini, G.Wade, R.C.Costi, M.P.

(2011) Proc.Natl.Acad.Sci.USA 108: E542-E549

  • DOI: 10.1073/pnas.1104829108
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human thymidylate synthase is a homodimeric enzyme that plays a key role in DNA synthesis and is a target for several clinically important anticancer drugs that bind to its active site. We have designed peptides to specifically target its dimer inter ...

    Human thymidylate synthase is a homodimeric enzyme that plays a key role in DNA synthesis and is a target for several clinically important anticancer drugs that bind to its active site. We have designed peptides to specifically target its dimer interface. Here we show through X-ray diffraction, spectroscopic, kinetic, and calorimetric evidence that the peptides do indeed bind at the interface of the dimeric protein and stabilize its di-inactive form. The "LR" peptide binds at a previously unknown binding site and shows a previously undescribed mechanism for the allosteric inhibition of a homodimeric enzyme. It inhibits the intracellular enzyme in ovarian cancer cells and reduces cellular growth at low micromolar concentrations in both cisplatin-sensitive and -resistant cells without causing protein overexpression. This peptide demonstrates the potential of allosteric inhibition of hTS for overcoming platinum drug resistance in ovarian cancer.


    Organizational Affiliation

    Department of Pharmaceutical Sciences, via Campi 183, University of Modena and Reggio Emilia, 41126 Modena, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidylate synthase
A
325Homo 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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Thymidylate synthase
B
325Homo 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
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Synthetic peptide LR
D
8N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000970
Query on PRD_000970
DSynthetic peptide LRPolypeptide / Inhibitor

--

Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SCH
Query on SCH
A, B
L-PEPTIDE LINKINGC4 H9 N O2 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.188 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 96.109α = 90.00
b = 96.109β = 90.00
c = 82.240γ = 120.00
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
MOLREPphasing
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-06-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-07-24
    Type: Database references