2FTO

Y94F mutant of thymidylate synthase bound to thymidine-5'-phosphate and 10-propargyl-5,8-dideazafolid acid

• PDB DOI: https://doi.org/10.2210/pdb2FTO/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-01-24 Released: 2006-05-02 
• Deposition Author(s): Roberts, S.A., Montfort, W.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.179 
• R-Value Work: 0.158 
• R-Value Observed: 0.159 

Literature

Structure of the Y94F mutant of Escherichia coli thymidylate synthase.

Roberts, S.A., Hyatt, D.C., Honts, J.E., Changchien, L., Maley, G.F., Maley, F., Montfort, W.R.

(2006) Acta Crystallogr Sect F Struct Biol Cryst Commun 62: 840-843

• PubMed: 16946460 
• DOI: https://doi.org/10.1107/S1744309106029691
• Primary Citation of Related Structures:  
  2FTN, 2FTO


• PubMed Abstract: 
  

  Tyr94 of Escherichia coli thymidylate synthase is thought to be involved, either directly or by activation of a water molecule, in the abstraction of a proton from C5 of the 2'-deoxyuridine 5'-monophosphate (dUMP) substrate. Mutation of Tyr94 leads to a 400-fold loss in catalytic activity. The structure of the Y94F mutant has been determined in the native state and as a ternary complex with thymidine 5'-monophosphate (dTMP) and 10-propargyl 5,8-dideazafolate (PDDF). There are no structural changes ascribable to the mutation other than loss of a water molecule hydrogen bonded to the tyrosine OH, which is consistent with a catalytic role for the phenolic OH.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 31.53 kDa 
• Atom Count: 2,326 
• Modelled Residue Count: 264 
• Deposited Residue Count: 264 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A [auth X]	264	Escherichia coli	Mutation(s): 2  Gene Names: thyA EC: 2.1.1.45
UniProt
Find proteins for P0A884 (Escherichia coli (strain K12)) Explore P0A884  Go to UniProtKB:  P0A884

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CB3	E [auth X]	10-PROPARGYL-5,8-DIDEAZAFOLIC ACID C24 H23 N5 O6 LTKHPMDRMUCUEB-IBGZPJMESA-N
TMP	D [auth X]	THYMIDINE-5'-PHOSPHATE C10 H15 N2 O8 P GYOZYWVXFNDGLU-XLPZGREQSA-N
PO4	B [auth X], C [auth X]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CXM	A [auth X]	L-PEPTIDE LINKING	C6 H11 N O4 S		MET

Binding Affinity Annotations
ID	Source	Binding Affinity
CB3	BindingDB:  2FTO	IC50: 60 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.179 
• R-Value Work: 0.158 
• R-Value Observed: 0.159 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.08	α = 90
b = 72.08	β = 90
c = 115.21	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MADNESS	data reduction
PROCOR	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-05-02 
Deposition Author(s): Roberts, S.A., Montfort, W.R.

Revision History  

• Version 1.0: 2006-05-02
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2018-04-18
  Changes: Data collection
• Version 1.5: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.6: 2024-11-06
  Changes: Data collection, Structure summary