2CFA

Structure of viral flavin-dependant thymidylate synthase ThyX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Catalytic Mechanism and Structure of Viral Flavin-Dependent Thymidylate Synthase Thyx.

Graziani, S.Bernauer, J.Skouloubris, S.Graille, M.Zhou, C.-Z.Marchand, C.Decottignies, P.Van Tilbeurgh, H.Myllykallio, H.Liebl, U.

(2006) J.Biol.Chem. 281: 24048

  • DOI: 10.1074/jbc.M600745200

  • PubMed Abstract: 
  • By using biochemical and structural analyses, we have investigated the catalytic mechanism of the recently discovered flavin-dependent thymidylate synthase ThyX from Paramecium bursaria chlorella virus-1 (PBCV-1). Site-directed mutagenesis experiment ...

    By using biochemical and structural analyses, we have investigated the catalytic mechanism of the recently discovered flavin-dependent thymidylate synthase ThyX from Paramecium bursaria chlorella virus-1 (PBCV-1). Site-directed mutagenesis experiments have identified several residues implicated in either NADPH oxidation or deprotonation activity of PBCV-1 ThyX. Chemical modification by diethyl pyrocarbonate and mass spectroscopic analyses identified a histidine residue (His53) crucial for NADPH oxidation and located in the vicinity of the redox active N-5 atom of the FAD ring system. Moreover, we observed that the conformation of active site key residues of PBCV-1 ThyX differs from earlier reported ThyX structures, suggesting structural changes during catalysis. Steady-state kinetic analyses support a reaction mechanism where ThyX catalysis proceeds via formation of distinct ternary complexes without formation of a methyl enzyme intermediate.


    Organizational Affiliation

    CNRS, UMR 7645, Laboratory of Optics and Biosciences, Ecole Polytechnique, 91128 Palaiseau, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDYLATE SYNTHASE
A
217Paramecium bursaria Chlorella virus 1Mutation(s): 0 
EC: 2.1.1.148
Find proteins for O41156 (Paramecium bursaria Chlorella virus 1)
Go to UniProtKB:  O41156
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
THYMIDYLATE SYNTHASE
B
217Paramecium bursaria Chlorella virus 1Mutation(s): 0 
EC: 2.1.1.148
Find proteins for O41156 (Paramecium bursaria Chlorella virus 1)
Go to UniProtKB:  O41156
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CME
Query on CME
A, B
L-PEPTIDE LINKINGC5 H11 N O3 S2CYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 69.264α = 90.00
b = 76.991β = 90.00
c = 93.437γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-16
    Type: Initial release
  • Version 1.1: 2013-07-17
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance