Dihydropyrimidine Dehydrogenase (DPD) C671S Mutant Soaked with Thymine and NADPH Anaerobically

Experimental Data Snapshot

  • Resolution: 1.69 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

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This is version 1.2 of the entry. See complete history


Perturbing the Movement of Hydrogens to Delineate and Assign Events in the Reductive Activation and Turnover of Porcine Dihydropyrimidine Dehydrogenase.

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

(2021) Biochemistry 60: 1764-1775

  • DOI: https://doi.org/10.1021/acs.biochem.1c00243
  • Primary Citation of Related Structures:  
    7M31, 7M32

  • PubMed Abstract: 

    The native function of dihydropyrimidine dehydrogenase (DPD) is to reduce the 5,6-vinylic bond of pyrimidines uracil and thymine with electrons obtained from NADPH. NADPH and pyrimidines bind at separate active sites separated by ∼60 Å that are bridged by four Fe 4 S 4 centers. We have shown that DPD undergoes reductive activation, taking up two electrons from NADPH [Beaupre, B. A., et al. (2020) Biochemistry 59 , 2419-2431]. pH studies indicate that the rate of turnover is not controlled by the protonation state of the general acid, cysteine 671. The activation of the C671 variants is delineated into two phases particularly at low pH values. Spectral deconvolution of the delineated reductive activation reaction reveals that the initial phase results in the accumulation of charge transfer absorption added to the binding difference spectrum for NADPH. The second phase results in reduction of one of the two flavins. X-ray crystal structure analysis of the C671S variant soaked with NADPH and the slow substrate, thymine, in a low-oxygen atmosphere resolved the presumed activated form of the enzyme that has the FMN cofactor reduced. These data reveal that charge transfer arises from the proximity of the NADPH and FAD bases and that the ensuing flavin is a result of rapid transfer of electrons to the FMN without accumulation of reduced forms of the FAD or Fe 4 S 4 centers. These data suggest that the slow rate of turnover of DPD is governed by the movement of a mobile structural feature that carries the C671 residue.

  • Organizational Affiliation

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

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): 1 
Gene Names: DPYD
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
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
HA [auth D],
I [auth A],
Q [auth B],
Z [auth C]
C27 H33 N9 O15 P2
NAP (Subject of Investigation/LOI)
Query on NAP

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AA [auth C],
IA [auth D],
J [auth A],
R [auth B]
C21 H28 N7 O17 P3
FMN (Subject of Investigation/LOI)
Query on FMN

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CA [auth C],
K [auth A],
KA [auth D],
T [auth B]
C17 H21 N4 O9 P
SF4 (Subject of Investigation/LOI)
Query on SF4

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DA [auth D]
E [auth A]
EA [auth D]
F [auth A]
FA [auth D]
DA [auth D],
E [auth A],
EA [auth D],
F [auth A],
FA [auth D],
G [auth A],
GA [auth D],
H [auth A],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
V [auth C],
W [auth C],
X [auth C],
Y [auth C]
Fe4 S4
TDR (Subject of Investigation/LOI)
Query on TDR

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BA [auth C],
JA [auth D],
L [auth A],
S [auth B]
C5 H6 N2 O2
PRO (Subject of Investigation/LOI)
Query on PRO

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C5 H9 N O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.69 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.04α = 90
b = 159.56β = 95.75
c = 162.95γ = 90
Software Package:
Software NamePurpose
xia2data scaling
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: 2021-06-09
    Type: Initial release
  • Version 1.1: 2021-06-23
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Advisory, Data collection, Database references, Refinement description