2AAZ

Cryptococcus neoformans thymidylate synthase complexed with substrate and an antifolate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.290 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The structure of Cryptococcus neoformans thymidylate synthase suggests strategies for using target dynamics for species-specific inhibition.

Finer-Moore, J.S.Anderson, A.C.O'Neil, R.H.Costi, M.P.Ferrari, S.Krucinski, J.Stroud, R.M.

(2005) Acta Crystallogr.,Sect.D 61: 1320-1334

  • DOI: 10.1107/S0907444905022638
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The ternary complex crystal structures of Cryptococcus neoformans and Escherichia coli thymidylate synthase (TS) suggest mechanisms of species-specific inhibition of a highly conserved protein. The 2.1 Angstrom structure of C. neoformans TS cocrystal ...

    The ternary complex crystal structures of Cryptococcus neoformans and Escherichia coli thymidylate synthase (TS) suggest mechanisms of species-specific inhibition of a highly conserved protein. The 2.1 Angstrom structure of C. neoformans TS cocrystallized with substrate and the cofactor analog CB3717 shows that the binding sites for substrate and cofactor are highly conserved with respect to human TS, but that the structure of the cofactor-binding site of C. neoformans TS is less constrained by surrounding residues. This feature might allow C. neoformans TS to form TS-dUMP-inhibitor complexes with a greater range of antifolates than human TS. 3',3''-Dibromophenol-4-chloro-1,8-naphthalein (GA9) selectively inhibits both E. coli TS and C. neoformans TS (K(i) = 4 microM) over human TS (K(i) > 245 microM). The E. coli TS-dUMP-GA9 complex is in an open conformation, similar to that of the apoenzyme crystal structure. The GA9-binding site overlaps the binding site of the pABA-glutamyl moiety of the cofactor. The fact that human apoTS can adopt an unusual fold in which the GA9-binding site is disordered may explain the poor affinity of GA9 for the human enzyme. These observations highlight the critical need to incorporate multiple target conformations in any computational attempt to facilitate drug discovery.


    Related Citations: 
    • Structure-based design of inhibitors specific for bacterial thymidylate synthase
      Stout, T.J.,Tondi, D.,Rinaldi, M.,Barlocco, D.,Pecorari, P.,Santi, D.V.,Kuntz, I.D.,Stroud, R.M.,Shoichet, B.K.,Costi, M.P.
      (1999) Biochemistry 38: 1607
    • Phthalein derivatives as a new tool for selectivity in thymidylate synthase inhibition
      Costi, P.M.,Rinaldi, M.,Tondi, D.,Pecorari, P.,Barlocco, D.,Ghelli, S.,Stroud, R.M.,Santi, D.V.,Stout, T.J.,Musiu, C.,Marangiu, E.M.,Pani, A.,Congiu, D.,Loi, G.A.,La Colla, P.
      (1999) J.Med.Chem. 42: 2112


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th Street, Room S412B, San Francisco, CA 94143-2240, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidylate synthase
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
317Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565)Mutation(s): 0 
Gene Names: TMP1
EC: 2.1.1.45
Find proteins for P0CS12 (Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565))
Go to UniProtKB:  P0CS12
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CB3
Query on CB3

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
10-PROPARGYL-5,8-DIDEAZAFOLIC ACID
C24 H23 N5 O6
LTKHPMDRMUCUEB-IBGZPJMESA-N
 Ligand Interaction
UMP
Query on UMP

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
DUMP
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.08 Å
  • R-Value Free: 0.305 
  • R-Value Work: 0.290 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 179.400α = 90.00
b = 179.500β = 89.80
c = 209.100γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-12-06
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2015-09-09
    Type: Version format compliance
  • Version 1.4: 2018-02-14
    Type: Experimental preparation