Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36.88 kDa 
• Atom Count: 2638 
• Residue Count: 316 
• Unique protein chains: 1

1VZA

THYMIDYLATE SYNTHASE E60D MUTANT BINARY COMPLEX WITH 2'-DEOXYURIDINE 5'-MONOPHOSPHATE (DUMP)

• DOI: 10.2210/pdb1VZA/pdb

• Classification: METHYLTRANSFERASE
• Organism(s): Lacticaseibacillus casei
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1996-09-18 Released: 1997-03-12 
• Deposition Author(s): Birdsall, D.L., Finer-Moore, J., Stroud, R.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.210 
• R-Value Observed: 0.210 

Literature

The separate effects of E60Q in Lactobacillus casei thymidylate synthase delineate between mechanisms for formation of intermediates in catalysis.

Birdsall, D.L., Huang, W., Santi, D.V., Stroud, R.M., Finer-Moore, J.

(1998) Protein Eng 11: 171-183

• PubMed: 9613841 
• DOI: 10.1093/protein/11.3.171
• Primary Citation of Related Structures:  
  1VZE, 1VZD, 1VZC, 1VZB, 1VZA


• PubMed Abstract: 
  

X-Ray crystal structures of Lactobacillus casei thymidylate synthase (TS) mutant complexes of E60D with dUMP, and E60Q with dUMP or FdUMP, as well as ternary complexes with folate analog inhibitor CB3717, are described. The structures we report address the decrease in rate of formation of ternary complexes in the E60 mutants. Structures of ternary complexes of L.casei TS mimic ligand-bound TS just prior to covalent bond formation between ligands and protein. Ternary complex structures of L.casei TS E60Q show the ligands are not optimally aligned for making the necessary covalent bonds. Since CB3717 is an analog of the open, activated form of the cofactor, these structures suggest that the slow rate of ternary complex formation in E60 mutants is at least partly the result of impaired alignment of ligands in the active site after binding and activation of the cofactor. Binary complexes of TS E60Q and TS E60D with substrate (dUMP) show no change in dUMP position or occupancy. These results are consistent with the fact that Kd(dUMP) and Km(dUMP) are almost the same, and the rates of folate-independent debromination of 5-bromo-dUMP are even higher than for wild type TS.

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Related Citations: 

• Refined Structures of Substrate-Bound and Phosphate-Bound Thymidylate Synthase from Lactobacillus Casei
  Finer-Moore, J., Fauman, E.B., Foster, P.G., Perry, K.M., Santi, D.V., Stroud, R.M.
  (1993) J Mol Biol 232: 1101

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
THYMIDYLATE SYNTHASE	A	316	Lacticaseibacillus casei	Mutation(s): 1  Gene Names: THYMIDYLATE SYNTHASE, thyA EC: 2.1.1.45
Find proteins for P00469 (Lactobacillus casei) Explore P00469  Go to UniProtKB:  P00469

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UMP	A	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C9 H13 N2 O8 P JSRLJPSBLDHEIO-SHYZEUOFSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Work: 0.210 
• R-Value Observed: 0.210 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 79.1	α = 90
b = 79.1	β = 90
c = 230.3	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
PROCESS	data reduction
PROCESS	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1996-09-18 
• Released Date: 1997-03-12 
Deposition Author(s): Birdsall, D.L., Finer-Moore, J., Stroud, R.M.

Revision History 

• Version 1.0: 1997-03-12
  Type: Initial release
  
• Version 1.1: 2008-03-04
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance