1H7X

Dihydropyrimidine dehydrogenase (DPD) from pig, ternary complex of a mutant enzyme (C671A), NADPH and 5-fluorouracil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 

wwPDB Validation 3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Crystal Structure of Dihydropyrimidine Dehydrogenase, a Major Determinant of the Pharmacokinetics of the Anti-Cancer Drug 5-Fluorouracil

Dobritzsch, D.Schneider, G.Schnackerz, K.D.Lindqvist, Y.

(2001) EMBO J 20: 650

  • DOI: 10.1093/emboj/20.4.650
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Dihydropyrimidine dehydrogenase catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. Its controlled inhibition has become an adjunct target for cancer the ...

    Dihydropyrimidine dehydrogenase catalyzes the first step in pyrimidine degradation: the NADPH-dependent reduction of uracil and thymine to the corresponding 5,6-dihydropyrimidines. Its controlled inhibition has become an adjunct target for cancer therapy, since the enzyme is also responsible for the rapid breakdown of the chemotherapeutic drug 5-fluorouracil. The crystal structure of the homodimeric pig liver enzyme (2x 111 kDa) determined at 1.9 A resolution reveals a highly modular subunit organization, consisting of five domains with different folds. Dihydropyrimidine dehydrogenase contains two FAD, two FMN and eight [4Fe-4S] clusters, arranged in two electron transfer chains that pass the dimer interface twice. Two of the Fe-S clusters show a hitherto unobserved coordination involving a glutamine residue. The ternary complex of an inactive mutant of the enzyme with bound NADPH and 5-fluorouracil reveals the architecture of the substrate-binding sites and residues responsible for recognition and binding of the drug.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Study of Pig Liver Dihydropyrimidine Dehydrogenase
      Dobritzsch, D., Persson, K., Schneider, G., Lindqvist, Y.
      (2001) Acta Crystallogr D Biol Crystallogr 57: 153

    Organizational Affiliation

    Division of Molecular Structural Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DIHYDROPYRIMIDINE DEHYDROGENASE
A, B, C, D
1025Sus scrofaMutation(s): 1 
Gene Names: DPYD
EC: 1.3.1.2
Find proteins for Q28943 (Sus scrofa)
Go to UniProtKB:  Q28943
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download CCD File 
A, B, C, D
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
NDP
Query on NDP

Download CCD File 
A, B, C, D
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
FMN
Query on FMN

Download CCD File 
A, B, C, D
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
SF4
Query on SF4

Download CCD File 
A, B, C, D
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
URF
Query on URF

Download CCD File 
A, B, C, D
5-FLUOROURACIL
C4 H3 F N2 O2
GHASVSINZRGABV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.95α = 90
b = 159.29β = 96.04
c = 163.57γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-02-23
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2018-01-17
    Changes: Advisory, Atomic model, Data collection, Derived calculations
  • Version 2.1: 2018-02-07
    Changes: Source and taxonomy