PDBsum entry 4xec

Oxidoreductase/oxidoreductase inhibitor

PDB id: 4xec

Contents

Protein chain

157 a.a.

Ligands

06U

ACT

NDP

Waters ×38

PDB id:

4xec

Name:

Oxidoreductase/oxidoreductase inhibitor

Title:

Staphylococcus aureus dihydrofolate reductase complexed with NADPH and 6-ethyl-5-[(3r)-3-[3-methoxy-5-(pyridin-4-yl)phenyl]but-1-yn-1- yl]pyrimidine-2,4-diamine (ucp1061)

Structure:

Dihydrofolate reductase. Chain: x. Synonym: dhfr. Engineered: yes

Source:

Staphylococcus aureus. Organism_taxid: 1280. Atcc: 29213. Gene: fola. Expressed in: escherichia coli. Expression_system_taxid: 511693. Expression_system_variant: de3.

Resolution:

2.69Å R-factor: 0.164 R-free: 0.233

Authors:

S.M.Reeve,A.C.Anderson

Key ref:

S.Keshipeddy et al. (2015). Nonracemic Antifolates Stereoselectively Recruit Alternate Cofactors and Overcome Resistance in S. aureus. J Am Chem Soc, 137, 8983-8990. PubMed id: 26098608 DOI: 10.1021/jacs.5b01442

Date:

23-Dec-14 Release date: 22-Jul-15

Protein chain

P0A017  (DYR_STAAU) -  Dihydrofolate reductase from Staphylococcus aureus

Seq: 159 a.a.

Struc: 157 a.a.

Enzyme reactions

• Enzyme class: E.C.1.5.1.3 - dihydrofolate reductase.
• Pathway: Folate Coenzymes
• Reaction: (6S)-5,6,7,8-tetrahydrofolate + NADP⁺ = 7,8-dihydrofolate + NADPH + H⁺

(6S)-5,6,7,8-tetrahydrofolate + NADP(+) (Bound ligand (Het Group name = NDP) corresponds exactly) = 7,8-dihydrofolate + NADPH + H(+)

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

reference

DOI no: 10.1021/jacs.5b01442

J Am Chem Soc 137:8983-8990 (2015)

PubMed id: 26098608

Nonracemic Antifolates Stereoselectively Recruit Alternate Cofactors and Overcome Resistance in S. aureus.

S.Keshipeddy, S.M.Reeve, A.C.Anderson, D.L.Wright.

ABSTRACT

While antifolates such as Bactrim (trimethoprim-sulfamethoxazole; TMP-SMX) continue to play an important role in treating community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA), resistance-conferring mutations, specifically F98Y of dihydrofolate reductase (DHFR), have arisen and compromise continued use. In an attempt to extend the lifetime of this important class, we have developed a class of propargyl-linked antifolates (PLAs) that exhibit potent inhibition of the enzyme and bacterial strains. Probing the role of the configuration at the single propargylic stereocenter in these inhibitors required us to develop a new approach to nonracemic 3-aryl-1-butyne building blocks by the pairwise use of asymmetric conjugate addition and aldehyde dehydration protocols. Using this new route, a series of nonracemic PLA inhibitors was prepared and shown to possess potent enzyme inhibition (IC50 values <50 nM), antibacterial effects (several with MIC values <1 μg/mL) and to form stable ternary complexes with both wild-type and resistant mutants. Unexpectedly, crystal structures of a pair of individual enantiomers in the wild-type DHFR revealed that the single change in configuration of the stereocenter drove the selection of an alternative NADPH cofactor, with the minor α-anomer appearing with R-27. Remarkably, this cofactor switching becomes much more prevalent when the F98Y mutation is present. The observation of cofactor site plasticity leads to a postulate for the structural basis of TMP resistance in DHFR and also suggests design strategies that can be used to target these resistant enzymes.