PDBsum entry 7ljs

Flavoprotein

PDB id: 7ljs

Contents

Protein chains

1005 a.a.

Ligands

SF4 ×16

FMN ×4

FAD ×4

Y3G ×4

Waters ×2171

PDB id:

7ljs

Name:

Flavoprotein

Title:

Porcine dihydropyrimidine dehydrogenase (dpd) complexed with 5- ethynyluracil (5eu) - open form

Structure:

Dihydropyrimidine dehydrogenase [nadp(+)]. Chain: a, b, c, d. Synonym: dpd,dihydrothymine dehydrogenase,dihydrouracil dehydrogenase. Engineered: yes

Source:

Sus scrofa. Pig. Organism_taxid: 9823. Gene: dpyd. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.00Å R-factor: 0.175 R-free: 0.229

Authors:

A.Butrin,D.Forouzesh,B.Beaupre,Z.Wawrzak,D.Liu,G.Moran

Key ref:

D.C.Forouzesh et al. (2021). The Interaction of Porcine Dihydropyrimidine Dehydrogenase with the Chemotherapy Sensitizer: 5-Ethynyluracil. Biochemistry, 60, 1120-1132. PubMed id: 33755421 DOI: 10.1021/acs.biochem.1c00096

Date:

30-Jan-21 Release date: 07-Apr-21

Protein chains

Q28943  (DPYD_PIG) -  Dihydropyrimidine dehydrogenase [NADP(+)] from Sus scrofa

Seq: 1025 a.a.

Struc: 1005 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.1.3.1.2 - dihydropyrimidine dehydrogenase (NADP(+)).
• Reaction: 5,6-dihydrouracil + NADP⁺ = uracil + NADPH + H⁺

5,6-dihydrouracil (Bound ligand (Het Group name = Y3G) matches with 80.00% similarity) + NADP(+) (Bound ligand (Het Group name = FAD) matches with 71.19% similarity) = uracil + NADPH + H(+)

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

reference

DOI no: 10.1021/acs.biochem.1c00096

Biochemistry 60:1120-1132 (2021)

PubMed id: 33755421

The Interaction of Porcine Dihydropyrimidine Dehydrogenase with the Chemotherapy Sensitizer: 5-Ethynyluracil.

D.C.Forouzesh, B.A.Beaupre, A.Butrin, Z.Wawrzak, D.Liu, G.R.Moran.

ABSTRACT

Dihydropyrimidine dehydrogenase (DPD) is a complex enzyme that reduces the 5,6-vinylic bond of pyrimidines, uracil, and thymine. 5-Fluorouracil (5FU) is also a substrate for DPD and a common chemotherapeutic agent used to treat numerous cancers. The reduction of 5FU to 5-fluoro-5,6-dihydrouracil negates its toxicity and efficacy. Patients with high DPD activity levels typically have poor outcomes when treated with 5FU. DPD is thus a central mitigating factor in the treatment of a variety of cancers. 5-Ethynyluracil (5EU) covalently inactivates DPD by cross-linking with the active-site general acid cysteine in the pyrimidine binding site. This reaction is dependent on the simultaneous binding of 5EU and nicotinamide adenine dinucleotide phosphate (NADPH). This ternary complex induces DPD to become activated by taking up two electrons from the NADPH. The covalent inactivation of DPD by 5EU occurs concomitantly with this reductive activation with a rate constant of ∼0.2 s^-1. This k_inact value is correlated with the rate of reduction of one of the two flavin cofactors and the localization of a mobile loop in the pyrimidine active site that places the cysteine that serves as the general acid in catalysis proximal to the 5EU ethynyl group. Efficient cross-linking is reliant on enzyme activation, but this process appears to also have a conformational aspect in that nonreductive NADPH analogues can also induce a partial inactivation. Cross-linking then renders DPD inactive by severing the proton-coupled electron transfer mechanism that transmits electrons 56 Å across the protein.