4KNZ

Thymidylate synthase ternary complex with dUMP AND CB3717


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.131 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mg(2+) binds to the surface of thymidylate synthase and affects hydride transfer at the interior active site.

Wang, Z.Sapienza, P.J.Abeysinghe, T.Luzum, C.Lee, A.L.Finer-Moore, J.S.Stroud, R.M.Kohen, A.

(2013) J.Am.Chem.Soc. 135: 7583-7592

  • DOI: 10.1021/ja400761x
  • Primary Citation of Related Structures:  4IW5

  • PubMed Abstract: 
  • Thymidylate synthase (TSase) produces the sole intracellular de novo source of thymidine (i.e., the DNA base T) and thus is a common target for antibiotic and anticancer drugs. Mg(2+) has been reported to affect TSase activity, but the mechanism of t ...

    Thymidylate synthase (TSase) produces the sole intracellular de novo source of thymidine (i.e., the DNA base T) and thus is a common target for antibiotic and anticancer drugs. Mg(2+) has been reported to affect TSase activity, but the mechanism of this interaction has not been investigated. Here we show that Mg(2+) binds to the surface of Escherichia coli TSase and affects the kinetics of hydride transfer at the interior active site (16 Å away). Examination of the crystal structures identifies a Mg(2+) near the glutamyl moiety of the folate cofactor, providing the first structural evidence for Mg(2+) binding to TSase. The kinetics and NMR relaxation experiments suggest that the weak binding of Mg(2+) to the protein surface stabilizes the closed conformation of the ternary enzyme complex and reduces the entropy of activation on the hydride transfer step. Mg(2+) accelerates the hydride transfer by ~7-fold but does not affect the magnitude or temperature dependence of the intrinsic kinetic isotope effect. These results suggest that Mg(2+) facilitates the protein motions that bring the hydride donor and acceptor together, but it does not change the tunneling ready state of the hydride transfer. These findings highlight how variations in cellular Mg(2+) concentration can modulate enzyme activity through long-range interactions in the protein, rather than binding at the active site. The interaction of Mg(2+) with the glutamyl tail of the folate cofactor and nonconserved residues of bacterial TSase may assist in designing antifolates with polyglutamyl substitutes as species-specific antibiotic drugs.


    Related Citations: 
    • The Role of Protein Dynamics in Thymidylate Synthase Catalysis: Variants of Conserved 2'-Deoxyuridine 5'-Monophosphate (Dump)-Binding Tyr-261.
      Newby, Z.,Lee, T.T.,Morse, R.J.,Liu, Y.,Liu, L.,Venkatraman, P.,Santi, D.V.,Finer-Moore, J.S.,Stroud, R.M.
      (2006) Biochemistry 45: 7415
    • A Remote Mutation Affects the Hydride Transfer by Disrupting Concerted Protein Motions in Thymidylate Synthase.
      Wang, Z.,Abeysinghe, T.,Finer-Moore, J.S.,Stroud, R.M.,Kohen, A.
      (2012) J.Am.Chem.Soc. 134: 17722


    Organizational Affiliation

    Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidylate synthase
A, B
264Escherichia coli (strain K12)Gene Names: thyA
EC: 2.1.1.45
Find proteins for P0A884 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A884
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CB3
Query on CB3

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

Download SDF File 
Download CCD File 
A, B
2'-deoxy-5'-uridylic acid
C9 H15 N2 O8 P
WQQZADPPRABIFU-SHYZEUOFSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CXM
Query on CXM
A, B
L-PEPTIDE LINKINGC6 H11 N O4 SMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UMCKd: 8500 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.154 
  • R-Value Work: 0.131 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 125.410α = 90.00
b = 125.410β = 90.00
c = 66.580γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
ELVESrefinement
SCALEPACKdata scaling
EPMRphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2013-06-05
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description