1NJE

THYMIDYLATE SYNTHASE WITH 2'-DEOXYCYTIDINE 5'-MONOPHOSPHATE (DCMP)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Partitioning roles of side chains in affinity, orientation, and catalysis with structures for mutant complexes: asparagine-229 in thymidylate synthase.

Finer-Moore, J.S.Liu, L.Schafmeister, C.E.Birdsall, D.L.Mau, T.Santi, D.V.Stroud, R.M.

(1996) Biochemistry 35: 5125-5136

  • DOI: 10.1021/bi952751x
  • Primary Citation of Related Structures:  1NJA, 1NJB, 1NJC, 1NJD

  • PubMed Abstract: 
  • Thymidylate synthase (TS) methylates only dUMP, not dCMP. The crystal structure of TS.dCMP shows sCMP 4-NH2 excluded from the space between Asn-229 and His-199 by the hydrogen bonding and steric properties and Asn-229. Consequently, 6-C of dCMP is ov ...

    Thymidylate synthase (TS) methylates only dUMP, not dCMP. The crystal structure of TS.dCMP shows sCMP 4-NH2 excluded from the space between Asn-229 and His-199 by the hydrogen bonding and steric properties and Asn-229. Consequently, 6-C of dCMP is over 4 A from the active site sulfhydryl. The Asn-229 side chain is prevented from flipping 180 degrees to and orientation the could hydrogen bond to dCMP by a hydrogen bond network between conserved residues. Thus, the specific binding of dUMP by TS results from occlusion of competing substrates by steric and electronic effects of residues in the active site cavity. When Asn-229 is replaced by a cysteine, the Cys-229 S gamma rotates out of the active site, and the mutant enzyme binds both dCMP and dUMP tightly but does not methylate dCMP. Thus simply admitting dCMP into the dUMP binding site of TS is not sufficient for methylation of dCMP. Structures of nucleotide complexes of TS N229D provide a reasonable explanation for the preferential methylation of dCMP instead of dUMP by this mutant. In TS N229D.dCMP, Asp-229 forms hydrogen bonds to 3-N and 40NH2 of dCMP. Neither the Asp-229 carboxyl moiety nor ordered water appears to hydrogen bond to 4-O of dUMP. Hydrogen bonds to 4-O (or 4-NH2) have been proposed to stabilize reaction intermediates. If their absence in TS N229D.dUMP persists in the ternary complex, it could explain the 10(4)-fold decrease in kcat/Km for dUMP.


    Related Citations: 
    • Stereochemistry of a Multistep/Bipartite Methyl Transfer Reaction: Thymidylate Synthase
      Stroud, R.M.,Finer-Moore, J.S.
      (1993) Faseb J. 7: 671
    • Refined Structures of Substrate-Bound and Phosphate-Bound Thymidylate Synthase from Lactobacillus Casei
      Finer-Moore, J.,Fauman, E.B.,Foster, P.G.,Perry, K.M.,Santi, D.V.,Stroud, R.M.
      (1993) J.Mol.Biol. 232: 1101
    • Mutation of Asparagine 229 to Aspartate in Thymidylate Synthase Converts the Enzyme to a Deoxycytidylate Methylase
      Liu, L.,Santi, D.V.
      (1992) Biochemistry 31: 5100
    • Exclusion of 2'-Deoxycytidine 5'-Monophosphate by Asparagine 229 of Thymidylate Synthase
      Liu, L.,Santi, D.V.
      (1993) Biochemistry 32: 9263


    Organizational Affiliation

    Department of Biochemistry and Biophysics, University of California, San Francisco 94143-0448, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDYLATE SYNTHASE
A
316Lactobacillus caseiGene Names: thyA
EC: 2.1.1.45
Find proteins for P00469 (Lactobacillus casei)
Go to UniProtKB:  P00469
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DCM
Query on DCM

Download SDF File 
Download CCD File 
A
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
C9 H14 N3 O7 P
NCMVOABPESMRCP-SHYZEUOFSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DCMKd: 160000 nM BINDINGMOAD
DCMKd: 160000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Work: 0.213 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 78.500α = 90.00
b = 78.500β = 90.00
c = 242.300γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
R-AXISdata reduction
X-PLORphasing
X-PLORmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-07-11
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance