2FTO | pdb_00002fto

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 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

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 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 
• Modeled 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 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

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