1H7X | pdb_00001h7x

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

PDB DOI: https://doi.org/10.2210/pdb1H7X/pdb

Classification: ELECTRON TRANSFER
Organism(s): Sus scrofa
Expression System: Escherichia coli DH5[alpha]
Mutation(s): Yes

Deposited: 2001-01-19 Released: 2001-02-23
Deposition Author(s): Dobritzsch, D., Schneider, G., Schnackerz, K.D., Lindqvist, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free:
0.192 (Depositor), 0.190 (DCC)
R-Value Work:
0.171 (Depositor), 0.168 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 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

PubMed: 11179210 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1093/emboj/20.4.650
Primary Citation Related Structures:
1H7W, 1H7X

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 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 460.38 kDa
Atom Count: 36,037
Modeled Residue Count: 4,073
Deposited Residue Count: 4,100
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DIHYDROPYRIMIDINE DEHYDROGENASE	A, B, C, D	1,025	Sus scrofa	Mutation(s): 1 Gene Names: DPYD EC: 1.3.1.2
UniProt
Find proteins for Q28943 (Sus scrofa) Explore Q28943 Go to UniProtKB: Q28943
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q28943
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain R [auth B] SDF format, chain J [auth A] SDF format, chain HA [auth D] MOL2 format, chain Z [auth C] MOL2 format, chain R [auth B] MOL2 format, chain J [auth A] MOL2 format, chain HA [auth D] mmCIF format, chain Z [auth C] mmCIF format, chain R [auth B] mmCIF format, chain J [auth A] mmCIF format, chain HA [auth D]	HA [auth D], J [auth A], R [auth B], Z [auth C]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain HA [auth D] Focus chain J [auth A] Focus chain R [auth B] Focus chain Z [auth C] Interactions & Density Focus chain HA [auth D] Focus chain J [auth A] Focus chain R [auth B] Focus chain Z [auth C]
NDP Query on NDP Download:Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain S [auth B] SDF format, chain IA [auth D] SDF format, chain AA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain S [auth B] MOL2 format, chain IA [auth D] MOL2 format, chain AA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain S [auth B] mmCIF format, chain IA [auth D] mmCIF format, chain AA [auth C]	AA [auth C], IA [auth D], K [auth A], S [auth B]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₃₀ N₇ O₁₇ P₃ ACFIXJIJDZMPPO-NNYOXOHSSA-N		Interactions Focus chain AA [auth C] Focus chain IA [auth D] Focus chain K [auth A] Focus chain S [auth B] Interactions & Density Focus chain AA [auth C] Focus chain IA [auth D] Focus chain K [auth A] Focus chain S [auth B]
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain Y [auth C] SDF format, chain I [auth A] SDF format, chain GA [auth D] MOL2 format, chain Q [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain I [auth A] MOL2 format, chain GA [auth D] mmCIF format, chain Q [auth B] mmCIF format, chain Y [auth C] mmCIF format, chain I [auth A] mmCIF format, chain GA [auth D]	GA [auth D], I [auth A], Q [auth B], Y [auth C]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain GA [auth D] Focus chain I [auth A] Focus chain Q [auth B] Focus chain Y [auth C] Interactions & Density Focus chain GA [auth D] Focus chain I [auth A] Focus chain Q [auth B] Focus chain Y [auth C]
SF4 Query on SF4 Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain H [auth A] SDF format, chain M [auth B] SDF format, chain U [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain V [auth C] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain G [auth A] SDF format, chain FA [auth D] SDF format, chain F [auth A] SDF format, chain EA [auth D] SDF format, chain E [auth A] SDF format, chain DA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] MOL2 format, chain U [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain V [auth C] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth D] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B] mmCIF format, chain U [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth C] mmCIF format, chain V [auth C] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth D] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth D] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth D]	CA [auth D] DA [auth D] E [auth A] EA [auth D] F [auth A] CA [auth D], DA [auth D], E [auth A], EA [auth D], F [auth A], FA [auth D], G [auth A], H [auth A], M [auth B], N [auth B], O [auth B], P [auth B], U [auth C], V [auth C], W [auth C], X [auth C]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain E [auth A] Focus chain EA [auth D] Focus chain F [auth A] Focus chain FA [auth D] Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]
URF Query on URF Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain L [auth A] SDF format, chain JA [auth D] SDF format, chain BA [auth C] MOL2 format, chain T [auth B] MOL2 format, chain L [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain BA [auth C] mmCIF format, chain T [auth B] mmCIF format, chain L [auth A] mmCIF format, chain JA [auth D] mmCIF format, chain BA [auth C]	BA [auth C], JA [auth D], L [auth A], T [auth B]	5-FLUOROURACIL C₄ H₃ F N₂ O₂ GHASVSINZRGABV-UHFFFAOYSA-N		Interactions Focus chain BA [auth C] Focus chain JA [auth D] Focus chain L [auth A] Focus chain T [auth B] Interactions & Density Focus chain BA [auth C] Focus chain JA [auth D] Focus chain L [auth A] Focus chain T [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.01 Å
R-Value Free: 0.192 (Depositor), 0.190 (DCC)
R-Value Work: 0.171 (Depositor), 0.168 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.95	α = 90
b = 159.29	β = 96.04
c = 163.57	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2001-02-23

Deposition Author(s):

Revision History (Full details and data files)

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
Version 2.2: 2024-05-01
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description