1NCE

Crystal structure of a ternary complex of E. coli thymidylate synthase D169C with dUMP and the antifolate CB3717


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The only active mutant of thymidylate synthase D169, a residue far from the site of methyl transfer, demonstrates the exquisite nature of enzyme specificity.

Birdsall, D.L.Finer-Moore, J.Stroud, R.M.

(2003) Protein Eng 16: 229-240

  • DOI: 10.1093/proeng/gzg020
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Cysteine is the only variant of D169, a cofactor-binding residue in thymidylate synthase, that shows in vivo activity. The 2.4 A crystal structure of Escherichia coli thymidylate synthase D169C in a complex with dUMP and the antifolate CB3717 shows it to be an asymmetric dimer, with only one active site covalently bonded to dUMP ...

    Cysteine is the only variant of D169, a cofactor-binding residue in thymidylate synthase, that shows in vivo activity. The 2.4 A crystal structure of Escherichia coli thymidylate synthase D169C in a complex with dUMP and the antifolate CB3717 shows it to be an asymmetric dimer, with only one active site covalently bonded to dUMP. At the active site with covalently bound substrate, C169 S gamma adopts the roles of both carboxyl oxygens of D169, making a 3.6 A S...H[bond]N hydrogen bond to 3-NH of CB3717 and a 3.4 A water-mediated hydrogen bond to H212. Analogous hydrogen bonds formed during the enzyme reaction are important for cofactor binding and are postulated to contribute to catalysis. The C169 side chain is likely to be ionized, making it a better hydrogen bond acceptor than a neutral sulfhydryl group. At the second active site, C169 S gamma makes a shorter (3 A) hydrogen bond to the 3-NH of CB3717, CB3717 is approximately 1.5 A out of its binding site and there is no covalent bond between dUMP and the catalytic cysteine. Changes to partitioning among productive and non-productive conformations of reaction intermediates may contribute as much, if not more, to the diminished activity of this mutant than reduced stabilization of transition states.


    Related Citations: 
    • D221 in thymidylate synthase controls conformation change, and thereby opening of the imidazolidine
      Sage, C.R., Michelitsch, M.D., Stout, T.J., Biermann, D., Nissen, R., Finer-Moore, J., Stroud, R.M.
      (1998) Biochemistry 37: 13893
    • 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 and Biophysics, University of California at San Francisco, San Francisco, CA 94143-0448, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidylate synthaseA, B264Escherichia coliEscherichia coli O157:H7
This entity is chimeric
Mutation(s): 2 
Gene Names: THYA OR B2827 OR Z4144 OR ECS3684
EC: 2.1.1.45
Find proteins for P0A884 (Escherichia coli (strain K12))
Explore P0A884 
Go to UniProtKB:  P0A884
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CB3
Query on CB3

Download CCD File 
A, B
10-PROPARGYL-5,8-DIDEAZAFOLIC ACID
C24 H23 N5 O6
LTKHPMDRMUCUEB-IBGZPJMESA-N
 Ligand Interaction
UMP
Query on UMP

Download CCD File 
A, B
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CXM
Query on CXM
A,BL-PEPTIDE LINKINGC6 H11 N O4 SMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CB3IC50:  60   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.1α = 90
b = 127.1β = 90
c = 68.1γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-12-25
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Database references