1DNA

D221(169)N MUTANT DOES NOT PROMOTE OPENING OF THE COFACTOR IMIDAZOLIDINE RING


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 13893-13901

  • DOI: 10.1021/bi9810510
  • Primary Citation of Related Structures:  1BJG

  • PubMed Abstract: 
  • In thymidylate synthase (TS), the invariant residue Asp-221 provides the only side chain that hydrogen bonds to the pterin ring of the cofactor, 5,10-methylene-5,6,7,8-tetrahydrofolate. All mutants of D221 except cysteine abolish activity. We have de ...

    In thymidylate synthase (TS), the invariant residue Asp-221 provides the only side chain that hydrogen bonds to the pterin ring of the cofactor, 5,10-methylene-5,6,7,8-tetrahydrofolate. All mutants of D221 except cysteine abolish activity. We have determined the crystal structures of two ternary complexes of the Escherichia coli mutant D221N. In a complex with dUMP and the antifolate 10-propargyl-5,8-dideazafolate (CB3717), dUMP is covalently bound to the active site cysteine, as usual. CB3717, which has no imidazolidine ring, is also bound in the usual productive orientation, but is less ordered than in wild-type complexes. The side chain of Asn-221 still hydrogen bonds to N3 of the quinazoline ring of CB3717, which must be in the enol form. In contrast, the structure of D221N with 5-fluoro-dUMP and 5,10-methylene-5,6,7, 8-tetrahydrofolate shows the cofactor bound in two partially occupied, nonproductive binding sites. In both binding modes, the cofactor has a closed imidazolidine ring and adopts the solution conformation of the unbound cofactor. In one of the binding sites, the pterin ring is turned around such that Asn-221 hydrogen bonds to the unprotonated N1 instead of the protonated N3 of the cofactor. This orientation blocks the conformational change required for forming covalent ternary complexes. Taken together, the two crystal structures suggest that the hydrogen bond between the side chain of Asp-221 and N3 of the cofactor is most critical during the early steps of cofactor binding, where it enforces the correct orientation of the pterin ring. Proper orientation of the cofactor appears to be a prerequisite for opening the imidazolidine ring prior to formation of the covalent steady-state intermediate in catalysis.


    Related Citations: 
    • Stereochemistry of a Multistep/Bipartite Methyl Transfer Reaction: Thymidylate Synthase
      Stroud, R.M.,Finer-Moore, J.S.
      (1993) Faseb J. 7: 671
    • 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 94143-0448, 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
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
UMP
Query on UMP

Download SDF File 
Download CCD File 
A, B
2'-DEOXYURIDINE 5'-MONOPHOSPHATE
DUMP
C9 H13 N2 O8 P
JSRLJPSBLDHEIO-SHYZEUOFSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CXM
Query on CXM
A, B
L-PEPTIDE LINKINGC6 H11 N O4 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.180 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 127.221α = 90.00
b = 127.221β = 90.00
c = 68.178γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
SCALEPACKdata scaling
X-PLORphasing
X-PLORmodel building
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-11-04
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance