4GEV

E. coli thymidylate synthase Y209W variant in complex with substrate and a cofactor analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.128 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A remote mutation affects the hydride transfer by disrupting concerted protein motions in thymidylate synthase.

Wang, Z.Abeysinghe, T.Finer-Moore, J.S.Stroud, R.M.Kohen, A.

(2012) J Am Chem Soc 134: 17722-17730

  • DOI: 10.1021/ja307859m
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The role of protein flexibility in enzyme-catalyzed activation of chemical bonds is an evolving perspective in enzymology. Here we examine the role of protein motions in the hydride transfer reaction catalyzed by thymidylate synthase (TSase). Being r ...

    The role of protein flexibility in enzyme-catalyzed activation of chemical bonds is an evolving perspective in enzymology. Here we examine the role of protein motions in the hydride transfer reaction catalyzed by thymidylate synthase (TSase). Being remote from the chemical reaction site, the Y209W mutation of Escherichia coli TSase significantly reduces the protein activity, despite the remarkable similarity between the crystal structures of the wild-type and mutant enzymes with ligands representing their Michaelis complexes. The most conspicuous difference between these two crystal structures is in the anisotropic B-factors, which indicate disruption of the correlated atomic vibrations of protein residues in the mutant. This dynamically altered mutant allows a variety of small thiols to compete for the reaction intermediate that precedes the hydride transfer, indicating disruption of motions that preorganize the protein environment for this chemical step. Although the mutation causes higher enthalpy of activation of the hydride transfer, it only shows a small effect on the temperature dependence of the intrinsic KIE, suggesting marginal changes in the geometry and dynamics of the H-donor and -acceptor at the tunneling ready state. These observations suggest that the mutation disrupts the concerted motions that bring the H-donor and -acceptor together during the pre- and re-organization of the protein environment. The integrated structural and kinetic data allow us to probe the impact of protein motions on different time scales of the hydride transfer reaction within a complex enzymatic mechanism.


    Related Citations: 
    • The role of protein dynamics in thymidylate synthase catalysis: variants of conserved 2'-deoxyuridine 5'-monophosphate (dUMP)-binding Tyr-261.
      Newby, Z., Lee, T.T., Morse, R.J., Liu, Y., Liu, L., Venkatraman, P., Santi, D.V., Finer-Moore, J.S., Stroud, R.M.
      (2006) Biochemistry 45: 7415

    Organizational Affiliation

    Department of Chemistry, University of Iowa, Iowa City, Iowa 52242-1727, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thymidylate synthaseA, B264Escherichia coli K-12Mutation(s): 1 
Gene Names: b2827JW2795thyA
EC: 2.1.1.45
Find proteins for P0A884 (Escherichia coli (strain K12))
Explore P0A884 
Go to UniProtKB:  P0A884
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CB3
Query on CB3

Download CCD File 
A, B
10-PROPARGYL-5,8-DIDEAZAFOLIC ACID
C24 H23 N5 O6
LTKHPMDRMUCUEB-IBGZPJMESA-N
 Ligand Interaction
UMC
Query on UMC

Download CCD File 
A, B
2'-deoxy-5'-uridylic acid
C9 H15 N2 O8 P
WQQZADPPRABIFU-SHYZEUOFSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CXM
Query on CXM
A,BL-PEPTIDE LINKINGC6 H11 N O4 SMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CB3IC50:  60   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.151 
  • R-Value Work: 0.127 
  • R-Value Observed: 0.128 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.778α = 90
b = 125.778β = 90
c = 66.938γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
ELVESrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-08-29
    Type: Initial release
  • Version 1.1: 2012-10-17
    Changes: Database references
  • Version 1.2: 2012-11-07
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description