2TSR

THYMIDYLATE SYNTHASE FROM RAT IN TERNARY COMPLEX WITH DUMP AND TOMUDEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

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

  • DOI: 10.1021/bi981881d
  • Primary Citation of Related Structures:  

  • 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 ap ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDYLATE SYNTHASE
A, B, C, D
307Rattus norvegicusMutation(s): 0 
Gene Names: Tyms
EC: 2.1.1.45
Find proteins for P45352 (Rattus norvegicus)
Go to UniProtKB:  P45352
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D16
Query on D16

Download SDF File 
Download CCD File 
A, B, C, D
TOMUDEX
ZD1694; Raltitrexed
C21 H22 N4 O6 S
IVTVGDXNLFLDRM-HNNXBMFYSA-N
 Ligand Interaction
UMP
Query on UMP

Download SDF File 
Download CCD File 
A, B, C, D
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
DUMP
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
D16Ki: 29 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.162 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 99.700α = 90.00
b = 101.600β = 101.40
c = 140.800γ = 90.00
Software Package:
Software NamePurpose
CCP4data scaling
PROCORdata reduction
X-PLORrefinement
X-PLORphasing
X-PLORmodel building
ROTAVATAdata scaling
MADNESdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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