2TDD

STRUCTURES OF THYMIDYLATE SYNTHASE WITH A C-TERMINAL DELETION: ROLE OF THE C-TERMINUS IN ALIGNMENT OF D/UMP AND CH2H4FOLATE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Work: 0.190 

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This is version 1.2 of the entry. See complete history. 


Literature

Structures of thymidylate synthase with a C-terminal deletion: role of the C-terminus in alignment of 2'-deoxyuridine 5'-monophosphate and 5,10-methylenetetrahydrofolate.

Perry, K.M., Carreras, C.W., Chang, L.C., Santi, D.V., Stroud, R.M.

(1993) Biochemistry 32: 7116-7125

  • DOI: 10.1021/bi00079a007
  • Primary Citation of Related Structures:  
    1TDC, 1TDB, 1TDA, 2TDD

  • PubMed Abstract: 

    • Thymidylate synthase undergoes a major conformational change upon ligand binding, where the carboxyl terminus displays the largest movement (approximately 4 A). This movement from an "open" unliganded state to the "closed" complexed conformation plays a ...

    Thymidylate synthase undergoes a major conformational change upon ligand binding, where the carboxyl terminus displays the largest movement (approximately 4 A). This movement from an "open" unliganded state to the "closed" complexed conformation plays a crucial role in the correct orientation of substrates and in product formation. The mutant lacking the C-terminal valine (V316Am) of the enzyme is inactive. X-ray crystal structures of V316Am and its complexes with dUMP, FdUMP, and both FdUMP and CH2H4folate are described. The structures show that ligands are bound within the active site, but in different modes than those in analogous, wild-type thymidylate synthase structures. The 2.7-A binary complex structures of V316Am with FdUMP and dUMP show that the pyrimidine and ribose moieties of the nucleotides are pivoted approximately 20 degrees around the 3'-hydroxyl compared to dUMP in the wild-type enzyme. The 2.7-A crystal structure of V316Am complexed with cofactor, CH2H4folate, and the substrate analog, FdUMP, shows these ligands bound in an open conformation similar to that of the unliganded enzyme. In this ternary complex, the imidazolidine ring of the cofactor is open and has reacted with water to form 5-HOCH2H4folate. 5-HOCH2H4folate is structural evidence for the 5-iminium ion intermediate, which is the proposed reactive form of CH2H4folate. The altered ligand binding modes observed in the three V316Am complex structures open new venues for the design of novel TS inhibitors.

    Related Citations: 
    • Atomic Structure of Thymidylate Synthase: Target for Rational Drug Design
      Hardy, L.W., Finer-Moore, J.S., Montfort, W.R., Jones, M.O., Santi, D.V., Stroud, R.M.
      (1987) Science 235: 448
    Organizational Affiliation: 

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



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
THYMIDYLATE SYNTHASE A315Lacticaseibacillus caseiMutation(s): 0 
Gene Names: thyA
EC: 2.1.1.45
Find proteins for P00469 (Lactobacillus casei)
Explore P00469 
Go to UniProtKB:  P00469
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
THF
Query on THF
Download Ideal Coordinates CCD File 
A
5-HYDROXYMETHYLENE-6-HYDROFOLIC ACID
C20 H23 N7 O7
IIEPLRAFVCMHQF-STQMWFEESA-N		 Ligand Interaction
UFP
Query on UFP
Download Ideal Coordinates CCD File 
A
5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
C9 H12 F N2 O8 P
HFEKDTCAMMOLQP-RRKCRQDMSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
UFPKd:  0   nM  BindingDB
UFPKi:  0   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Work: 0.190 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.4α = 90
b = 78.4β = 90
c = 242.2γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-07-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance