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- PDB-1gt8: DIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, TERNARY COMPLEX W... -

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Basic information

Entry
Database: PDB / ID: 1gt8
TitleDIHYDROPYRIMIDINE DEHYDROGENASE (DPD) FROM PIG, TERNARY COMPLEX WITH NADPH AND URACIL-4-ACETIC ACID
ComponentsDIHYDROPYRIMIDINE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / ELECTRON TRANSFER / FLAVIN / IRON-SULFUR CLUSTERS / PYRIMIDINE CATABOLISM / 5-FLUOROURACIL DEGRADATION
Function / homology
Function and homology information


dihydropyrimidine dehydrogenase (NADP+) / uracil binding / thymidine catabolic process / dihydropyrimidine dehydrogenase (NADP+) activity / beta-alanine biosynthetic process / uracil catabolic process / thymine catabolic process / FMN binding / NADP binding / flavin adenine dinucleotide binding ...dihydropyrimidine dehydrogenase (NADP+) / uracil binding / thymidine catabolic process / dihydropyrimidine dehydrogenase (NADP+) activity / beta-alanine biosynthetic process / uracil catabolic process / thymine catabolic process / FMN binding / NADP binding / flavin adenine dinucleotide binding / 4 iron, 4 sulfur cluster binding / protein homodimerization activity / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Dihydroprymidine dehydrogenase domain II / Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster / Alpha-helical ferredoxin / 4Fe-4S dicluster domain / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Alpha-helical ferredoxin / Alpha-Beta Plaits - #20 / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / FAD/NAD(P)-binding domain ...Dihydroprymidine dehydrogenase domain II / Dihydroprymidine dehydrogenase domain II, 4Fe-4S cluster / Alpha-helical ferredoxin / 4Fe-4S dicluster domain / Fumarate Reductase Iron-sulfur Protein; Chain B, domain 2 / Alpha-helical ferredoxin / Alpha-Beta Plaits - #20 / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Aldolase class I / Aldolase-type TIM barrel / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / FLAVIN MONONUCLEOTIDE / Chem-NDP / IRON/SULFUR CLUSTER / URACIL-6-ACETIC ACID / Dihydropyrimidine dehydrogenase [NADP(+)]
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsDobritzsch, D. / Ricagno, S. / Schneider, G. / Schnackerz, K.D. / Lindqvist, Y.
Citation
Journal: J. Biol. Chem. / Year: 2002
Title: Crystal structure of the productive ternary complex of dihydropyrimidine dehydrogenase with NADPH and 5-iodouracil. Implications for mechanism of inhibition and electron transfer.
Authors: Dobritzsch, D. / Ricagno, S. / Schneider, G. / Schnackerz, K.D. / Lindqvist, Y.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and Preliminary X-Ray Study of Pig Liver Dihydropyrimidine Dehydrogenase
Authors: Dobritzsch, D. / Persson, K. / Schneider, G. / Lindqvist, Y.
History
DepositionJan 14, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 11, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 2.0Jan 23, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / citation / pdbx_struct_conn_angle
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _pdbx_struct_conn_angle.value
Revision 2.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF", "BF", "CF" AND "DF" IN EACH CHAIN ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AF", "BF", "CF" AND "DF" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL, THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDROPYRIMIDINE DEHYDROGENASE
B: DIHYDROPYRIMIDINE DEHYDROGENASE
C: DIHYDROPYRIMIDINE DEHYDROGENASE
D: DIHYDROPYRIMIDINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)460,66936
Polymers446,4134
Non-polymers14,25632
Water00
1
A: DIHYDROPYRIMIDINE DEHYDROGENASE
B: DIHYDROPYRIMIDINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,33518
Polymers223,2072
Non-polymers7,12816
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: DIHYDROPYRIMIDINE DEHYDROGENASE
D: DIHYDROPYRIMIDINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,33518
Polymers223,2072
Non-polymers7,12816
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)82.030, 159.530, 166.020
Angle α, β, γ (deg.)90.00, 97.16, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9999, 0.007, -0.0105), (0.0018, -0.7452, -0.6668), (-0.0125, -0.6668, 0.7451)118.6034, 174.0582, 67.3701
2given(1, 0.0056, 0.0042), (-0.0038, 0.791, -0.6118), (-0.0042, 0.6118, 0.791)-14.017, 14.2456, -27.1431
3given(-0.9999, -0.011, -0.0131), (0.0119, -0.9969, -0.0775), (-0.0122, -0.0776, 0.9969)103.1956, 194.4521, -79.8019

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
DIHYDROPYRIMIDINE DEHYDROGENASE / DPD / DHPDHASE / DIHYDROURACIL DEHYDROGENASE / DIHYDROTHYMINE DEHYDROGENASE


Mass: 111603.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SUS SCROFA (pig) / Organ: LIVER / Plasmid: PSE420 / Production host: Escherichia coli DH5[alpha] (bacteria)
References: UniProt: Q28943, dihydropyrimidine dehydrogenase (NADP+)

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Non-polymers , 5 types, 32 molecules

#2: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#6: Chemical
ChemComp-UAA / URACIL-6-ACETIC ACID / 6-CARBOXYMETHYLURACIL


Mass: 170.123 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6N2O4

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Details

Compound detailsINVOLVED IN THE CATABOLISM OF URACIL AND THYMIDINE LEADING TO THE FORMATION OF BETA-ALANINE. ...INVOLVED IN THE CATABOLISM OF URACIL AND THYMIDINE LEADING TO THE FORMATION OF BETA-ALANINE. CATALYSES THE REDUCTION OF URACIL AND THYMINE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 40.03 %
Crystal growpH: 7.5
Details: 100 MM SODIUM CITRATE PH 4.7, 16-20% POLYETHYLENE GLYCOL 6000, 1 MM DTT
Crystal grow
*PLUS
Temperature: 293 K / pH: 4.7 / Method: vapor diffusion / Details: Dobritzsch, D., (2001) Acta Crystallogr., 57, 153.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
117-22 %(w/v)PEG60001reservoir
210 mMdithiothreitol1reservoir
3100 mMsodium citrate1reservoirpH4.7
44.5 mg/mlDPD1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 12, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 62722 / % possible obs: 98.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 9.8
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.463 / Mean I/σ(I) obs: 2.6 / % possible all: 92.9
Reflection
*PLUS
Highest resolution: 3.3 Å / Rmerge(I) obs: 0.098
Reflection shell
*PLUS
Highest resolution: 3.3 Å / % possible obs: 92.9 %

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: DIHYDROPYRIMIDINE DEHYDROGENASE, TERNARY COMPLEX WITH 5-IODOURACIL AND NADPH, PH 7.5

Resolution: 3.3→29.75 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2857472 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE 6-8 C-TERMINAL RESIDUES AND A FEW LOOP-RESIDUES WERE NOT SEEN IN THE DENSITY DUE TO DISORDER
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1247 2 %RANDOM
Rwork0.214 ---
obs0.214 62701 98.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.230877 e/Å3
Displacement parametersBiso mean: 53.3 Å2
Baniso -1Baniso -2Baniso -3
1--12.56 Å20 Å25.59 Å2
2--18.76 Å20 Å2
3----6.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.57 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 3.3→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30884 0 704 0 31588
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d3.12
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSRms dev Biso : 2 Å2 / Rms dev position: 0.11 Å
LS refinement shellResolution: 3.3→3.45 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.341 154 2.1 %
Rwork0.294 7328 -
obs--94.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PG2.PARWATER.TOP
X-RAY DIFFRACTION3CIS_PEPTIDE.PARAMPG2.TOP
X-RAY DIFFRACTION4WATER_REP.PARAMSUBS.TOP
Refinement
*PLUS
Rfactor obs: 0.217 / Rfactor Rfree: 0.273 / Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0115
X-RAY DIFFRACTIONc_angle_deg1.48
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg3.12
LS refinement shell
*PLUS
Rfactor obs: 0.294

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