1TLC

THYMIDYLATE SYNTHASE COMPLEXED WITH DGMP AND FOLATE ANALOG 1843U89


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Promotion of purine nucleotide binding to thymidylate synthase by a potent folate analogue inhibitor, 1843U89.

Weichsel, A.Montfort, W.R.Ciesla, J.Maley, F.

(1995) Proc.Natl.Acad.Sci.USA 92: 3493-3497

  • DOI: 10.1073/pnas.92.8.3493

  • PubMed Abstract: 
  • A folate analogue, 1843U89 (U89), with potential as a chemotherapeutic agent due to its potent and specific inhibition of thymidylate synthase (TS; EC 2.1.1.45), greatly enhances not only the binding of 5-fluoro-2'-deoxyuridine 5'-monophosphate (FdUM ...

    A folate analogue, 1843U89 (U89), with potential as a chemotherapeutic agent due to its potent and specific inhibition of thymidylate synthase (TS; EC 2.1.1.45), greatly enhances not only the binding of 5-fluoro-2'-deoxyuridine 5'-monophosphate (FdUMP) and dUMP to Escherichia coli TS but also that of dGMP, GMP, dIMP, and IMP. Guanine nucleotide binding was first detected by CD analysis, which revealed a unique spectrum for the TS-dGMP-U89 ternary complex. The quantitative binding of dGMP relative to GMP, FdUMP, and dUMP was determined in the presence and absence of U89 by ultrafiltration analysis, which revealed that although the binding of GMP and dGMP could not be detected in the absence of U89 both were bound in its presence. The Kd for dGMP was about the same as that for dUMP and FdUMP, with binding of the latter two nucleotides being increased by two orders of magnitude by U89. An explanation for the binding of dGMP was provided by x-ray diffraction studies that revealed an extensive stacking interaction between the guanine of dGMP and the benzoquinazoline ring of U89 and hydrogen bonds similar to those involved in dUMP binding. In addition, binding energy was provided through a water molecule that formed hydrogen bonds to both N7 of dGMP and the hydroxyl of Tyr-94. Accommodation of the larger dGMP molecule was accomplished through a distortion of the active site and a shift of the deoxyribose moiety to a new position. These rearrangements also enabled the binding of GMP to occur by creating a pocket for the ribose 2' hydroxyl group, overcoming the normal TS discrimination against nucleotides containing the 2' hydroxyl.


    Related Citations: 
    • Structure, Multiple Site Binding, and Segmental Accommodation in Thymidylate Synthase on Binding Dump: And an Anti-Folate
      Montfort, W.R.,Perry, K.M.,Fauman, E.B.,Finer-Moore, J.S.,Maley, G.F.,Hardy, L.,Maley, F.,Stroud, R.M.
      (1990) Biochemistry 29: 6964


    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
265Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: thyA
EC: 2.1.1.45
Find proteins for P0A884 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A884
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGP
Query on DGP

Download SDF File 
Download CCD File 
A, B
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O7 P
LTFMZDNNPPEQNG-KVQBGUIXSA-N
 Ligand Interaction
F89
Query on F89

Download SDF File 
Download CCD File 
A, B
S)-2-(5(((1,2-DIHYDRO-3-METHYL-1-OXOBENZO(F)QUINAZOLIN-9-YL)METHYL)AMINO)1-OXO-2-ISOINDOLINYL)GLUTARIC ACID
FOLATE ANALOG 1843U89
C27 H24 N4 O6
BRVFNEZMTRVUGW-QFIPXVFZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FMT
Query on FMT
A, B
NON-POLYMERC H2 O2

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DGPKd: 76 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 127.140α = 90.00
b = 127.140β = 90.00
c = 67.860γ = 120.00
Software Package:
Software NamePurpose
MADNESdata reduction
PROCORdata reduction
FBSCALEdata reduction
GPRLSArefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-06-03
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2018-04-18
    Type: Data collection, Other