Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | 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)

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 143.31 kDa 
• Atom Count: 9367 
• Modelled Residue Count: 1124 
• Deposited Residue Count: 1228 
• Unique protein chains: 1

2TSR

THYMIDYLATE SYNTHASE FROM RAT IN TERNARY COMPLEX WITH DUMP AND TOMUDEX

• PDB DOI: 10.2210/pdb2TSR/pdb

• Classification: METHYLTRANSFERASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1998-06-19 Released: 1999-02-16 
• Deposition Author(s): Sotelo-Mundo, R.R., Ciesla, J., Dzik, J.M., Rode, W., Maley, F., Maley, G., Hardy, L.W., Montfort, W.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.222 
• R-Value Work: 0.162 
• R-Value Observed: 0.162 

Literature

Crystal structures of rat thymidylate synthase inhibited by Tomudex, a potent anticancer drug.

Sotelo-Mundo, R.R., Ciesla, J., Dzik, J.M., Rode, W., Maley, F., Maley, G.F., Hardy, L.W., Montfort, W.R.

(1999) Biochemistry 38: 1087-1094

• PubMed: 9894005 
• DOI: 10.1021/bi981881d
• Primary Citation of Related Structures:  
  1RTS, 2TSR


• PubMed Abstract: 
  

Two crystal structures of rat thymidylate synthase (TS) complexed with dUMP and the anticancer drug Tomudex (ZD1694) have been determined to resolutions of 3.3 and 2.6 A. Tomudex is one of several new antifolates targeted to TS and the first to be approved for clinical use. The structures represent the first views of any mammalian TS bound to ligands and suggest that the rat protein undergoes a ligand-induced conformational change similar to that of the Escherichia coli protein. Surprisingly, Tomudex does not induce the "closed" conformation in rat TS that is seen on binding to E. coli TS, resulting in inhibitor atoms that differ in position by more than 1.5 A. Several species-specific differences in sequence may be the reason for this. Phe 74 shifts to a new position in the rat complex and is in van der Waals contact with the inhibitor, while in the E. coli protein the equivalent amino acid (His 51) hydrogen bonds to the glutamate portion of the inhibitor. Amino acids Arg 101, Asn 106, and Met 305 make no contacts with the inhibitor in the open conformation, unlike the equivalent residues in the E. coli protein (Thr 78, Trp 83, and Val 262). dUMP binding is similar in both proteins, except that there is no covalent adduct to the active site cysteine (Cys 189) in the rat structures. Two insertions in the rat protein are clearly seen, but the N-termini (residues 1-20) and C-termini (residues 301-307) are disordered in both crystal forms.

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Organizational Affiliation: 

Department of Biochemistry, University of Arizona, Tucson 85721, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THYMIDYLATE SYNTHASE	A, B, C, D	307	Rattus norvegicus	Mutation(s): 0  Gene Names: Tyms EC: 2.1.1.45
UniProt
Find proteins for P45352 (Rattus norvegicus) Explore P45352  Go to UniProtKB:  P45352

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
D16	F [auth A], H [auth B], J [auth C], L [auth D]	TOMUDEX C21 H22 N4 O6 S IVTVGDXNLFLDRM-HNNXBMFYSA-N
UMP	E [auth A], G [auth B], I [auth C], K [auth D]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
D16	PDBBind:  2TSR	Ki: 29 (nM) from 1 assay(s)
	BindingDB:  2TSR	IC50: 2.90e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.222 
• R-Value Work: 0.162 
• R-Value Observed: 0.162 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.7	α = 90
b = 101.6	β = 101.4
c = 140.8	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
MADNES	data reduction
PROCOR	data reduction
CCP4	data scaling
ROTAVATA	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-06-19 
• Released Date: 1999-02-16 
Deposition Author(s): Sotelo-Mundo, R.R., Ciesla, J., Dzik, J.M., Rode, W., Maley, F., Maley, G., Hardy, L.W., Montfort, W.R.

Revision History  

• Version 1.0: 1999-02-16
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2012-10-10
  Changes: Non-polymer description
• Version 1.4: 2018-04-18
  Changes: Data collection, Other, Refinement description