1GTE

DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, BINARY COMPLEX WITH 5-IODOURACIL

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history. 


Literature

Crystal structure of the productive ternary complex of dihydropyrimidine dehydrogenase with NADPH and 5-iodouracil. Implications for mechanism of inhibition and electron transfer.

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

(2002) J Biol Chem 277: 13155-13166

  • DOI: 10.1074/jbc.M111877200
  • Primary Citation of Related Structures:  
    1GT8, 1GTE, 1GTH

  • PubMed Abstract: 

    • Dihydroprymidine dehydrogenase catalyzes the first and rate-limiting step in pyrimidine degradation by converting pyrimidines to the corresponding 5,6- dihydro compounds. The three-dimensional structures of a binary complex with the inhibitor 5-iodou ...

    Dihydroprymidine dehydrogenase catalyzes the first and rate-limiting step in pyrimidine degradation by converting pyrimidines to the corresponding 5,6- dihydro compounds. The three-dimensional structures of a binary complex with the inhibitor 5-iodouracil and two ternary complexes with NADPH and the inhibitors 5-iodouracil and uracil-4-acetic acid were determined by x-ray crystallography. In the ternary complexes, NADPH is bound in a catalytically competent fashion, with the nicotinamide ring in a position suitable for hydride transfer to FAD. The structures provide a complete picture of the electron transfer chain from NADPH to the substrate, 5-iodouracil, spanning a distance of 56 A and involving FAD, four [Fe-S] clusters, and FMN as cofactors. The crystallographic analysis further reveals that pyrimidine binding triggers a conformational change of a flexible active-site loop in the alpha/beta-barrel domain, resulting in placement of a catalytically crucial cysteine close to the bound substrate. Loop closure requires physiological pH, which is also necessary for correct binding of NADPH. Binding of the voluminous competitive inhibitor uracil-4-acetic acid prevents loop closure due to steric hindrance. The three-dimensional structure of the ternary complex enzyme-NADPH-5-iodouracil supports the proposal that this compound acts as a mechanism-based inhibitor, covalently modifying the active-site residue Cys-671, resulting in S-(hexahydro-2,4-dioxo-5-pyrimidinyl)cysteine.

    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, S-17177 Stockholm, Sweden.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DIHYDROPYRIMIDINE DEHYDROGENASEA, B, C, D1025Sus scrofaMutation(s): 0 
Gene Names: DPYD
EC: 1.3.1.2
Find proteins for Q28943 (Sus scrofa)
Explore Q28943 
Go to UniProtKB:  Q28943
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
Download Ideal Coordinates CCD File 
A, B, C, D
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
FMN
Query on FMN
Download Ideal Coordinates CCD File 
A, B, C, D
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N		 Ligand Interaction
SF4
Query on SF4
Download Ideal Coordinates CCD File 
A, B, C, D
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
IUR
Query on IUR
Download Ideal Coordinates CCD File 
A, B, C, D
5-IODOURACIL
C4 H3 I N2 O2
KSNXJLQDQOIRIP-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IURIC50:  220   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.71α = 90
b = 158.37β = 95.84
c = 162.33γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-04-11
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-02-07
    Changes: Source and taxonomy
  • Version 2.0: 2019-01-23
    Changes: Atomic model, Data collection, Database references, Derived calculations
  • Version 2.1: 2019-07-10
    Changes: Data collection
  • Version 2.2: 2019-07-24
    Changes: Data collection