7LJS

Porcine Dihydropyrimidine dehydrogenase (DPD) complexed with 5-Ethynyluracil (5EU) - Open Form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

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

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

(2021) Biochemistry 60: 1120-1132

  • DOI: https://doi.org/10.1021/acs.biochem.1c00096
  • Primary Citation of Related Structures:  
    7LJS, 7LJT, 7LJU

  • PubMed 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.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W Sheridan RoadChicago, Illinois 60660, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydropyrimidine dehydrogenase [NADP(+)]
A, B, C, D
1,025Sus scrofaMutation(s): 0 
Gene Names: DPYD
EC: 1.3.1.2
UniProt
Find proteins for Q28943 (Sus scrofa)
Explore Q28943 
Go to UniProtKB:  Q28943
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ28943
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
EA [auth D],
J [auth A],
Q [auth B],
X [auth C]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
FMN (Subject of Investigation/LOI)
Query on FMN

Download Ideal Coordinates CCD File 
DA [auth D],
I [auth A],
P [auth B],
W [auth C]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
CA [auth D]
E [auth A]
F [auth A]
AA [auth D],
BA [auth D],
CA [auth D],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
Z [auth D]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Y3G (Subject of Investigation/LOI)
Query on Y3G

Download Ideal Coordinates CCD File 
FA [auth D],
K [auth A],
R [auth B],
Y [auth C]
5-ethynylpyrimidine-2,4(1H,3H)-dione
C6 H4 N2 O2
JOZGNYDSEBIJDH-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.031α = 90
b = 160.046β = 95.95
c = 164.074γ = 90
Software Package:
Software NamePurpose
xia2data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-04-07
    Type: Initial release
  • Version 1.1: 2021-04-28
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description