PDBsum entry 1syn

Transferase (methyltransferase)

PDB id: 1syn

Contents

Protein chains

265 a.a. *

Ligands

UMP ×2

F89 ×2

Waters ×174

* Residue conservation analysis

PDB id:

1syn

Name:

Transferase (methyltransferase)

Title:

E. Coli thymidylate synthase in complex with bw1843u89 and 2'- deoxyuridine 5'-monophosphate (dump)

Structure:

Thymidylate synthase. Chain: a, b. Ec: 2.1.1.45

Source:

Escherichia coli. Organism_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.196 R-free: 0.258

Authors:

T.J.Stout,R.M.Stroud

Key ref:

T.J.Stout and R.M.Stroud (1996). The complex of the anti-cancer therapeutic, BW1843U89, with thymidylate synthase at 2.0 A resolution: implications for a new mode of inhibition. Structure, 4, 67-77. PubMed id: 8805515 DOI: 10.1016/S0969-2126(96)00010-X

Date:

19-Sep-95 Release date: 29-Jan-96

Protein chains

P0A884  (TYSY_ECOLI) -  Thymidylate synthase from Escherichia coli (strain K12)

Seq: 264 a.a.

Struc: 265 a.a.

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 = UMP) corresponds exactly) = 7,8-dihydrofolate (Bound ligand (Het Group name = F89) matches with 46.81% similarity) + dTMP

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

reference

DOI no: 10.1016/S0969-2126(96)00010-X

Structure 4:67-77 (1996)

PubMed id: 8805515

The complex of the anti-cancer therapeutic, BW1843U89, with thymidylate synthase at 2.0 A resolution: implications for a new mode of inhibition.

T.J.Stout, R.M.Stroud.

ABSTRACT

BACKGROUND: Thymidylate synthase (TS) is critical to DNA synthesis as it catalyzes the rate limiting step in the only biosynthetic pathway for deoxythymidine monophosphate (dTMP) production. TS is therefore an important target for anti-proliferative and anti-cancer drug design. The TS enzymatic mechanism involves the reductive methylation of the substrate, deoxyuridine monophosphate (dUMP), by transfer of a methylene group from the co-factor, methylenetetrahydrofolate (CH2H4folate), resulting in the production of deoxythymidine monophosphate (dTMP) and dihydrofolate (H2folate). Previous drug design efforts based on co-factor analogues have produced good inhibitors of TS, but poor bioavailability and toxicity have limited their usefulness. BW1843U89, a folate analogue, is a recently developed compound which is an exceptionally strong inhibitor (Ki = 0.09 nM), has good bioavailability and in clinical trials thus far has not demonstrated significant toxicity. RESULTS: We report the crystal structure of E. coli TS in ternary complex with dUMP and BW1843U89 at 2.0 A resolution. Although the benzoquinazoline ring system of the inhibitor binds to TS in much the same manner as previously determined for H2folate and CB3717, the larger size of the ligand is accommodated by the enzyme through a local distortion of the active site, that is not strictly conserved in both monomers in the asymmetric unit. Several conserved waters that had been previously implicated in mechanistic roles have been displaced. CONCLUSIONS: BW1843U89 forms a ternary complex with dUMP and completes with CH2H4 folate at the active site. Inhibition of TS by BW1843U89 shows four unique aspects in its mechanism of action. BW1843U89 prevents the Michael addition of dUMP to Cys146, in contrast to the mechanisms implicated from crystallography of other quinazoline based inhibitors; displaces a catalytic water from the active site; reorders a peptide loop (Leu72-Trp83) in the active site; and is unique amongst the antifolates in inactivating TS at a stoichiometric ratio of one molecule per TS dimer. Thus, it exploits the principles of negative cooperativity that are increasingly being recognized in the catalytic mechanism of the enzyme per se. The structure suggests that this 'half-the-sites' effect is catalytic and not related to ligand binding. Therefore BW1843U89 is both a competitive inhibitor (at the binding site) and a non-competitive inhibitor at the other site.

Selected figure(s)

Figure 2.
Figure 2. Molecular Structures of BW1843U89, CB3717, ZD1694, dihydrofolate and methylenetetrahydrofolate. Figure 2. Molecular Structures of BW1843U89, CB3717, ZD1694, dihydrofolate and methylenetetrahydrofolate.

Figure 8.
Figure 8. Important interactions between BW1843U89 and surrounding constituents of the active site. The interaction between N14 and Glu58 presents a promising area for improved inhibitor design. Figure 8. Important interactions between BW1843U89 and surrounding constituents of the active site. The interaction between N14 and Glu58 presents a promising area for improved inhibitor design.

The above figures are reprinted by permission from Cell Press: Structure (1996, 4, 67-77) copyright 1996.

Figures were selected by an automated process.