PDBsum entry 1vzd

Methyltransferase

PDB id: 1vzd

Contents

Protein chain

316 a.a. *

Ligands

UFP

CB3

Waters ×378

* Residue conservation analysis

PDB id:

1vzd

Name:

Methyltransferase

Title:

L. Casei thymidylate synthase mutant e60q ternary complex with fdump and cb3717

Structure:

Thymidylate synthase. Chain: a. Synonym: ts, lcts. Engineered: yes. Mutation: yes

Source:

Lactobacillus casei. Organism_taxid: 1582. Gene: thymidylate synthase. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.50Å R-factor: 0.188

Authors:

D.L.Birdsall,J.Finer-Moore,R.M.Stroud

Key ref:

D.L.Birdsall et al. (1998). The separate effects of E60Q in Lactobacillus casei thymidylate synthase delineate between mechanisms for formation of intermediates in catalysis. Protein Eng, 11, 171-183. PubMed id: 9613841

Date:

18-Sep-96 Release date: 12-Mar-97

Protein chain

P00469  (TYSY_LACCA) -  Thymidylate synthase from Lacticaseibacillus casei

Seq: 316 a.a.

Struc: 316 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.2.1.1.45 - thymidylate synthase.
• Pathway: Folate Coenzymes
• Reaction: dUMP + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate = 7,8-dihydrofolate + dTMP

dUMP + (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate (Bound ligand (Het Group name = UFP) matches with 95.24% similarity) = 7,8-dihydrofolate (Bound ligand (Het Group name = CB3) matches with 48.89% similarity) + dTMP

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

Protein Eng 11:171-183 (1998)

PubMed id: 9613841

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

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

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.