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- PDB-2prl: The structures of apo- and inhibitor bound human dihydroorotate d... -

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Basic information

Entry
Database: PDB / ID: 2prl
TitleThe structures of apo- and inhibitor bound human dihydroorotate dehydrogenase reveal conformational flexibility within the inhibitor binding site
ComponentsDihydroorotate dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / protein inhibitor complex
Function / homology
Function and homology information


pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane ...pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / mitochondrial inner membrane / mitochondrion / nucleoplasm / cytosol
Similarity search - Function
Dihydroorotate dehydrogenase, class 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DECYLAMINE-N,N-DIMETHYL-N-OXIDE / FLAVIN MONONUCLEOTIDE / OROTIC ACID / 5-METHOXY-2-[(4-PHENOXYPHENYL)AMINO]BENZOIC ACID / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWalse, B. / Dufe, V.T. / Al-Karadaghi, S.
CitationJournal: Biochemistry / Year: 2008
Title: The structures of human dihydroorotate dehydrogenase with and without inhibitor reveal conformational flexibility in the inhibitor and substrate binding sites
Authors: Walse, B. / Dufe, V.T. / Svensson, B. / Fritzson, I. / Dahlberg, L. / Khairoullina, A. / Wellmar, U. / Al-Karadaghi, S.
History
DepositionMay 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 7, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2208
Polymers39,8571
Non-polymers1,3637
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.410, 90.410, 122.070
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Detailsbiological unit is a monomer

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Dihydroorotate dehydrogenase, mitochondrial / / E.C.1.3.3.1 / (Dihydroorotate oxidase / DHOdehase


Mass: 39856.535 Da / Num. of mol.: 1 / Mutation: N-terminus truncated
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: mitochondriaMitochondrion / Gene: DHODH / Plasmid: pET-19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q02127, EC: 1.3.99.11

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Non-polymers , 7 types, 238 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#5: Chemical ChemComp-ORO / OROTIC ACID / Orotic acid


Mass: 156.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N2O4
#6: Chemical ChemComp-R2C / 5-METHOXY-2-[(4-PHENOXYPHENYL)AMINO]BENZOIC ACID


Mass: 335.353 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17NO4
#7: Chemical ChemComp-DDQ / DECYLAMINE-N,N-DIMETHYL-N-OXIDE


Mass: 201.349 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H27NO
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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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: 3.61 Å3/Da / Density % sol: 65.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: DROPS WERE FORMED BY MIXING EQUAL AMOUNTS OF 18-24 MG/ML PROTEIN IN 100 MM HEPES PH 7.0, 400 MM NACL, 30% GLYCEROL, 1 MM EDTA AND 10 MM N,N- DIMETHYLUNDECYLAMIN-N-OXIDE (C11DAO) WITH A ...Details: DROPS WERE FORMED BY MIXING EQUAL AMOUNTS OF 18-24 MG/ML PROTEIN IN 100 MM HEPES PH 7.0, 400 MM NACL, 30% GLYCEROL, 1 MM EDTA AND 10 MM N,N- DIMETHYLUNDECYLAMIN-N-OXIDE (C11DAO) WITH A PRECIPITANT SOLUTION OF 0.1 M ACETATE PH 4.8 40 MM C11DAO, 20.8 MM N,-DIMETHYLDECYLAMINE-N-OXIDE (DDAO), 2 MM DIHYDROOROTATE (DHO) THE HANGING DROPS WERE INCUBATED AGAINST 0.5 ML RESERVOIR OF 0.1 M ACETATE PH 4.8, 1.6-2.2 M AMMONIUM SULFATE AND 30% GLYCEROL., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.092 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 27, 2004 / Details: mirrors
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.092 Å / Relative weight: 1
ReflectionResolution: 2.1→18.83 Å / Num. obs: 33570 / % possible obs: 98 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.487 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 12.17
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
2.1-2.20.3275.826848436799.5
2.2-2.30.2716.722493364399.2
2.3-2.40.2557.118935305599.1
2.4-2.60.2088.229772478598.9
2.6-2.70.1739.611800190098.9
2.7-30.1410.926614426998.4
3-40.08216.641760666597.6
4-50.0582414896238196.4
5-60.06122.86695106595.6
60.04728.68752144093.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
REFMAC5.2.0019refinement
REFMAC5.2.0019refinement
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1d3g

1d3g


Resolution: 2.1→18.83 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.923 / SU B: 5.642 / SU ML: 0.08 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.145 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19441 1678 5 %RANDOM
Rwork0.16771 ---
obs0.16907 31888 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.597 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20.08 Å20 Å2
2--0.16 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.1→18.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2805 0 94 231 3130
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222963
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2982.0184013
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6965376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.98422.992127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.66415500
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1911531
X-RAY DIFFRACTIONr_chiral_restr0.0710.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022250
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1910.21499
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22028
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2273
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.250
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4871.51897
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.75522929
X-RAY DIFFRACTIONr_scbond_it1.2731228
X-RAY DIFFRACTIONr_scangle_it2.0814.51079
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 122 -
Rwork0.164 2311 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
133.164113.0061-13.831152.1721-12.951927.06570.17350.27221.3518-0.2463-0.0943-3.5574-0.08982.5988-0.0792-0.0686-0.01290.08180.15510.01960.145553.204457.1639-6.2084
22.15290.47340.60291.05980.77463.58360.02160.09880.2843-0.179-0.0227-0.2891-0.40380.38670.0011-0.0357-0.03180.03420.00820.0497-0.000853.647748.2138-1.6786
31.048-0.11480.48480.68520.02950.7929-0.0093-0.00070.0480.0137-0.0104-0.0484-0.03320.14950.01970.0198-0.0102-0.00020.06310.01310.026146.907940.94837.9028
41.7204-0.47660.10760.8777-0.40311.3534-0.0133-0.0477-0.09730.0372-0.0425-0.04520.1299-0.00670.05590.01780.0054-0.00810.05790.01280.00549.990434.626518.5304
59.7682.252-12.90930.9619-3.56717.8493-0.3821.3266-0.6898-0.79020.15440.00851.1415-1.6280.22760.1176-0.0021-0.02980.2835-0.01110.033332.416926.62615.6801
63.2327-0.4141.63260.489-0.36662.2011-0.057-0.1549-0.14240.03180.0510.0330.0415-0.15730.0060.00270.00140.02720.04460.01040.004636.32334.303723.2697
70.8025-0.25250.1120.63050.09561.0815-0.0302-0.1193-0.01530.01510.00950.0575-0.0035-0.07040.0207-0.0050.0137-0.00980.04010.00010.023331.832942.36118.0704
81.1742-0.2477-0.09171.51420.19641.279-0.0128-0.02470.1932-0.0005-0.0076-0.0804-0.245-0.00250.02030.03980.0041-0.03120.0285-0.00070.041237.927254.66737.9272
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA30 - 361 - 7
2X-RAY DIFFRACTION2AA37 - 778 - 48
3X-RAY DIFFRACTION3AA78 - 14849 - 119
4X-RAY DIFFRACTION4AA149 - 216120 - 187
5X-RAY DIFFRACTION5AA217 - 231188 - 202
6X-RAY DIFFRACTION6AA232 - 271203 - 242
7X-RAY DIFFRACTION7AA272 - 346243 - 317
8X-RAY DIFFRACTION8AA347 - 396318 - 367

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