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

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Basic information

Entry
Database: PDB / ID: 2prh
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
Chem-238 / DECYLAMINE-N,N-DIMETHYL-N-OXIDE / FLAVIN MONONUCLEOTIDE / OROTIC ACID / Dihydroorotate dehydrogenase (quinone), mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...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 / 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

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0625
Polymers39,8571
Non-polymers1,2064
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.550, 90.550, 122.700
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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 , 5 types, 220 molecules

#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


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


Mass: 156.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N2O4
#4: Chemical ChemComp-238 / 6-CHLORO-2-(2'-FLUOROBIPHENYL-4-YL)-3-METHYLQUINOLINE-4-CARBOXYLIC ACID


Mass: 391.822 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H15ClFNO2
#5: Chemical ChemComp-DDQ / DECYLAMINE-N,N-DIMETHYL-N-OXIDE


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


Mass: 18.015 Da / Num. of mol.: 216 / 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: 3.64 Å3/Da / Density % sol: 66.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M acetate, 1.6-2.4M ammonium sulphate, 30% glycerol, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
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
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.092 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 29077 / Num. obs: 29077 / % possible obs: 75 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Biso Wilson estimate: 21.1 Å2 / Rmerge(I) obs: 0.118 / Rsym value: 0.12 / Net I/σ(I): 12
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 5.18 % / Rmerge(I) obs: 0.417 / Mean I/σ(I) obs: 4.61 / Num. unique all: 3134 / Rsym value: 0.309 / % possible all: 94

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D3G

1d3g


Resolution: 2.4→19.36 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.906 / SU B: 8.93 / SU ML: 0.119 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.234 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1160 5 %RANDOM
Rwork0.172 ---
all0.22 23197 --
obs0.174 23195 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.627 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.15 Å20 Å2
2--0.3 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 0 84 216 3027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222897
X-RAY DIFFRACTIONr_angle_refined_deg1.2632.0163928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7685362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.122.951122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44315485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4171529
X-RAY DIFFRACTIONr_chiral_restr0.080.2433
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022191
X-RAY DIFFRACTIONr_nbd_refined0.2130.21622
X-RAY DIFFRACTIONr_nbtor_refined0.2970.21955
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2131
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0910.27
X-RAY DIFFRACTIONr_mcbond_it0.4961.51842
X-RAY DIFFRACTIONr_mcangle_it0.80822858
X-RAY DIFFRACTIONr_scbond_it1.41631239
X-RAY DIFFRACTIONr_scangle_it2.3594.51069
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 83 -
Rwork0.175 1588 -
obs-1671 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)
17.36486.4592-16.896932.08-4.440842.8442-0.7659-1.69481.6273-1.43671.3005-2.12330.83161.9219-0.53460.211-0.02360.03540.2495-0.00110.24953.507756.8584-5.7871
21.64422.0853-0.30793.28261.364.86110.00040.4768-0.0394-0.45960.0729-0.32380.05560.7579-0.0732-0.0377-0.00340.06080.14760.0608-0.002353.651943.746-5.4281
322.1536-17.6863-13.975518.29119.58829.40671.09280.20142.3093-0.9063-0.0833-2.0973-1.24650.3302-1.00940.1142-0.1361-0.07550.2197-0.11180.312652.610257.59878.4639
40.9779-0.29680.55060.63540.1661.09910.03540.04440.0423-0.046-0.0055-0.0895-0.0360.2005-0.0299-0.0175-0.0079-0.00360.02130.00120.018347.041240.61377.9618
52.1065-0.0792-0.06031.2033-0.38161.8332-0.0493-0.1091-0.10590.1130.0445-0.12430.10380.12330.0048-0.02360.0112-0.02190.05150.0189-0.016850.805334.880319.3268
66.3841.0189-0.50912.2559-1.74331.36020.1313-0.1002-0.5995-0.45130.2040.1070.4128-0.4604-0.33540.04270.0102-0.03510.05430.04770.070737.53630.003924.8994
70.8711-0.24070.12080.607-0.11681.0898-0.0209-0.11350.00510.0183-0.05340.0214-0.0538-0.10270.0742-0.00970.0124-0.01730.0343-0.00840.007234.052342.55599.9186
83.24430.6268-0.8882.7072-0.46443.448-0.0819-0.17820.55980.12970.11850.0494-0.4742-0.1117-0.03670.05380.0852-0.0873-0.0397-0.02640.046733.466760.060911.5167
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
1130 - 361 - 7
2237 - 648 - 35
3365 - 7836 - 49
4479 - 14850 - 119
55149 - 211120 - 182
66212 - 245183 - 216
77246 - 368217 - 339
88369 - 396340 - 367

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