3TMS

PLASTIC ADAPTATION TOWARD MUTATIONS IN PROTEINS: STRUCTURAL COMPARISON OF THYMIDYLATE SYNTHASES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Plastic adaptation toward mutations in proteins: structural comparison of thymidylate synthases.

Perry, K.M.Fauman, E.B.Finer-Moore, J.S.Montfort, W.R.Maley, G.F.Maley, F.Stroud, R.M.

(1990) Proteins 8: 315-333

  • DOI: 10.1002/prot.340080406
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The structure of thymidylate synthase (TS) from Escherichia coli was solved from cubic crystals with a = 133 A grown under reducing conditions at pH 7.0, and refined to R = 22% at 2.1 A resolution. The structure is compared with that from Lactobacill ...

    The structure of thymidylate synthase (TS) from Escherichia coli was solved from cubic crystals with a = 133 A grown under reducing conditions at pH 7.0, and refined to R = 22% at 2.1 A resolution. The structure is compared with that from Lactobacillus casei solved to R = 21% at 2.3 A resolution. The structures are compared using a difference distance matrix, which identifies a common core of residues that retains the same relationship to one another in both species. After subtraction of the effects of a 50 amino acid insert present in Lactobacillus casei, differences in position of atoms correlate with temperature factors and with distance from the nearest substituted residue. The dependence of structural difference on thermal factor is parameterized and reflects both errors in coordinates that correlate with thermal factor, and the increased width of the energy well in which atoms of high thermal factor lie. The dependence of structural difference on distance from the nearest substitution also depends on thermal factors and shows an exponential dependence with half maximal effect at 3.0 A from the substitution. This represents the plastic accommodation of the protein which is parameterized in terms of thermal B factor and distance from a mutational change.


    Related Citations: 
    • Structure, Multiple Site Binding, and Segmental Accomodation in Thymidylate Synthase on Binding D/Ump and an Anti-Folate
      Montfort, W.R., Perry, K.M., Fauman, E.B., Finer-Moore, J.S., Maley, G.F., Hardy, L., Maley, F., Stroud, R.M.
      (1990) Biochemistry 29: 6964
    • Pairwise Specificity and Sequential Binding in Enzyme Catalysis: Thymidylate Synthase
      Finer-Moore, J.S., Montfort, W.R., Stroud, R.M.
      (1990) Biochemistry 29: 6977

    Organizational Affiliation

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



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THYMIDYLATE SYNTHASEA264Escherichia coliMutation(s): 0 
EC: 2.1.1.45
Find proteins for P0A884 (Escherichia coli (strain K12))
Explore P0A884 
Go to UniProtKB:  P0A884
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Work: 0.220 
  • Space Group: I 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133α = 90
b = 133β = 90
c = 133γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1991-10-15
    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