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PDBsum entry 1gt8
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Oxidoreductase PDB id
1gt8

 

 

 

 

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Contents
Protein chains
1017 a.a. *
Ligands
SF4 ×16
FMN ×4
FAD ×4
NDP ×4
UAA ×4
* Residue conservation analysis
PDB id:
1gt8
Name: Oxidoreductase
Title: Dihydropyrimidine dehydrogenase (dpd) from pig, ternary complex with NADPH and uracil-4-acetic acid
Structure: Dihydropyrimidine dehydrogenase. Chain: a, b, c, d. Synonym: dpd, dhpdhase, dihydrouracil dehydrogenase, dihydrothymine dehydrogenase. Engineered: yes
Source: Sus scrofa. Pig. Organism_taxid: 9823. Organ: liver. Expressed in: escherichia coli dh5[alpha]. Expression_system_taxid: 668369.
Biol. unit: Dimer (from PDB file)
Resolution:
3.30Å     R-factor:   0.214     R-free:   0.269
Authors: D.Dobritzsch,S.Ricagno,G.Schneider,K.D.Schnackerz,Y.Lindqvist
Key ref:
D.Dobritzsch et al. (2002). Crystal structure of the productive ternary complex of dihydropyrimidine dehydrogenase with NADPH and 5-iodouracil. Implications for mechanism of inhibition and electron transfer. J Biol Chem, 277, 13155-13166. PubMed id: 11796730 DOI: 10.1074/jbc.M111877200
Date:
14-Jan-02     Release date:   11-Apr-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q28943  (DPYD_PIG) -  Dihydropyrimidine dehydrogenase [NADP(+)] from Sus scrofa
Seq:
Struc: 		&nbsp
Seq:
Struc: 		&nbsp
Seq:
Struc: 		1025 a.a.
1017 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.1.3.1.2  - dihydropyrimidine dehydrogenase (NADP(+)).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 5,6-dihydrouracil + NADP+ = uracil + NADPH + H+
5,6-dihydrouracil
Bound ligand (Het Group name = UAA)
matches with 66.67% similarity 		+
NADP(+)
Bound ligand (Het Group name = NDP)
corresponds exactly 		= uracil
 + NADPH
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M111877200 J Biol Chem 277:13155-13166 (2002)
PubMed id: 11796730  
 
 
Crystal structure of the productive ternary complex of dihydropyrimidine dehydrogenase with NADPH and 5-iodouracil. Implications for mechanism of inhibition and electron transfer.
D.Dobritzsch, S.Ricagno, G.Schneider, K.D.Schnackerz, Y.Lindqvist.
 
  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-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 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.
 
  Selected figure(s)  
 
Figure 5.
Fig. 5. Conformational change of the active-site loop upon ligand binding and pH shift. The figure shows the pyrimidine-binding site in chain A of complex DPD·5IU·NADPH (pH 7.5). The active-site loop (comprising residues 670-682) and the adjacent residues Leu-669 and Ala-683 in the closed conformation (DPD·5IU·NADPH, pH 7.5) are shown in pink, with the loop residues 670, 671, and 673 given as ball-and-stick models (the carbon atoms of the modified Cys-671 (C671*) originating from 5IU are shown in brown; all others in pink). The same loop as observed in ligand-free DPD and DPD·5IU (pH 4.7) after superposition of domain IV with that of complex DPD·5IU·NADPH is shown in cyan. Here side chains are shown only for residues Ser-670 and Cys-671 (carbon atoms in cyan) to indicate their position in the open conformation. Ball-and-stick models of the cofactor FMN, substrate/inhibitor binding residues, and residue Lys-709 are given with carbon atoms in yellow. These residues do not change position or conformation upon ligand binding and pH shift. Hydrogen bond interactions of ligand binding residues Lys-709 and Ser-670 (as observed in DPD·5IU·NADPH (pH 7.5) and DPD·5IU (pH 4.7), respectively) are indicated by dotted lines. Labels in black mark residues placed at identical positions in both structures, and labels in cyan indicate the active-site-loop residues in ligand-free DPD. Active-site-loop residues of complex DPD·5IU·NADPH (pH 7.5) are labeled in pink. 		Figure 6.
Fig. 6. The electron transfer pathway between the ligand-binding sites. The cofactors FAD and FMN (carbon atoms in cyan) and the four [4Fe-4S] clusters creating the electron transfer chain between both flavins (iron atoms in magenta, sulfur atoms in green) as well as all amino acids located in van der Waals distance (3.8 Å) to the [4Fe-4S] clusters to atoms N5, N1, and C7M of FMN or to atoms N5, N1, and O[2] of FAD are shown as ball-and-stick models. Residues mentioned in the text are labeled. Amino acids with carbon atoms in yellow originate from the same subunit as FAD and FMN. Orange carbon atoms mark residues originating from the other subunit in the dimer. Hydrogen bond interactions mentioned in the text are indicated by dotted lines. For clarity, NADPH and the pyrimidine substrate are not shown.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 13155-13166) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference
  PubMed id Reference
17324113 X.Zhang, and R.B.Diasio (2007).
Regulation of human dihydropyrimidine dehydrogenase: implications in the pharmacogenetics of 5-FU-based chemotherapy.
  Pharmacogenomics, 8, 257-265.  
16595627 A.Osterman (2006).
A hidden metabolic pathway exposed.
  Proc Natl Acad Sci U S A, 103, 5637-5638.  
12703798 F.Peyrane, J.L.Fourrey, and P.Clivio (2003).
Thiation of 2'-deoxy-5,6-dihydropyrimidine nucleosides with Lawesson's reagent: characterisation of oxathiaphosphepane intermediates.
  Chem Commun (Camb), (), 736-737.  
12493833 M.S.Yousef, S.A.Clark, P.K.Pruett, T.Somasundaram, W.R.Ellington, and M.S.Chapman (2003).
Induced fit in guanidino kinases--comparison of substrate-free and transition state analog structures of arginine kinase.
  Protein Sci, 12, 103-111.
PDB code: 1m80
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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