Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 75.96 kDa 
• Atom Count: 4614 
• Residue Count: 534 
• Unique protein chains: 3

3N5E

Crystal Structure of human thymidylate synthase bound to a peptide inhibitor

• DOI: 10.2210/pdb3N5E/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-05-25 Released: 2011-06-08 
• Deposition Author(s): Pozzi, C., Cardinale, D., Guaitoli, G., Tondi, D., Luciani, R., Myllykallio, H., Ferrari, S., Costi, M.P., Mangani, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.221 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 

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 U S A 108: E542-E549

• PubMed: 21795601 
• DOI: 10.1073/pnas.1104829108
• Primary Citation of Related Structures:  
  3N5E, 3N5G


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A	325	Homo sapiens	Mutation(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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	B	325	Homo sapiens	Mutation(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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Synthetic peptide LR	D	8	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SCH	A	L-PEPTIDE LINKING	C4 H9 N O2 S2		CYS

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000970	D	Synthetic peptide LR	Polypeptide /  Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.26 Å
• R-Value Free: 0.221 
• R-Value Work: 0.188 
• R-Value Observed: 0.189 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.109	α = 90
b = 96.109	β = 90
c = 82.24	γ = 120

Software Package:

Software Name	Purpose
ADSC	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-05-25 
• Released Date: 2011-06-08 
Deposition Author(s): Pozzi, C., Cardinale, D., Guaitoli, G., Tondi, D., Luciani, R., Myllykallio, H., Ferrari, S., Costi, M.P., Mangani, S.

Revision History 

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