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- PDB-9vpv: Crystal structure of the C131A mutant of Trypanosoma brucei DHODH... -

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Basic information

Entry
Database: PDB / ID: 9vpv
TitleCrystal structure of the C131A mutant of Trypanosoma brucei DHODH in FMN-oxidized, orotate-bound form
ComponentsDihydroorotate dehydrogenase (fumarate)
KeywordsFLAVOPROTEIN / Ping-Pong Reaction Mechanism / Substrate/Product-enzyme interactions.
Function / homology
Function and homology information


dihydroorotate dehydrogenase (fumarate) / dihydroorotate dehydrogenase (fumarate) activity / fumarate metabolic process / dihydroorotate dehydrogenase activity / glycosome / ciliary plasm / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / nucleoplasm / cytoplasm
Similarity search - Function
Dihydroorotate dehydrogenase, class 1A / Dihydroorotate dehydrogenase, class 1/ 2 / : / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase-type TIM barrel
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / MALONATE ION / OROTIC ACID / Dihydroorotate dehydrogenase (fumarate)
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKubota, T. / Tani, O. / Yamasaki, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Mol.Biol. / Year: 2025
Title: Structural Basis of Redox-Dependent Affinities of Dihydroorotate Dehydrogenase for Its Substrates and Products.
Authors: Tani, O. / Kubota, T. / Yamasaki, T. / Hirokawa, T. / Furukawa, K. / Yamasaki, K.
History
DepositionJul 4, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 26, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase (fumarate)
B: Dihydroorotate dehydrogenase (fumarate)
C: Dihydroorotate dehydrogenase (fumarate)
D: Dihydroorotate dehydrogenase (fumarate)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,54325
Polymers137,7664
Non-polymers3,77621
Water5,801322
1
A: Dihydroorotate dehydrogenase (fumarate)
B: Dihydroorotate dehydrogenase (fumarate)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,82213
Polymers68,8832
Non-polymers1,93911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8540 Å2
ΔGint-20 kcal/mol
Surface area21030 Å2
MethodPISA
2
C: Dihydroorotate dehydrogenase (fumarate)
D: Dihydroorotate dehydrogenase (fumarate)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,72012
Polymers68,8832
Non-polymers1,83710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8440 Å2
ΔGint-21 kcal/mol
Surface area20960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.687, 146.531, 65.986
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-529-

HOH

21A-583-

HOH

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Components

#1: Protein
Dihydroorotate dehydrogenase (fumarate) / DHOD / DHODase / DHOdehase / Dihydroorotate oxidase


Mass: 34441.594 Da / Num. of mol.: 4 / Mutation: A115V,C131A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei brucei TREU927 (eukaryote)
Gene: Tb927.5.3830
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q57U83, dihydroorotate dehydrogenase (fumarate)
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ORO / OROTIC ACID


Mass: 156.096 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C5H4N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 49.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.2 M malonate, 0.1 M citrate (8.3), 100 mM Arg, 12.5 mM OA (co-crystallization).

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 53983 / % possible obs: 99.9 % / Redundancy: 7.13 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 18.8
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.493 / Num. unique obs: 2659

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XFV

5xfv


Resolution: 2.4→46.15 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / SU B: 9.564 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.419 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22997 2640 4.9 %RANDOM
Rwork0.18313 ---
obs0.18545 51287 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.739 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å20 Å2
2--0.01 Å20 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 2.4→46.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9402 0 259 322 9983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0129858
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169332
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.82413339
X-RAY DIFFRACTIONr_angle_other_deg0.4691.73221566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6951219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.548548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.012101633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0620.21475
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211312
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022132
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4772.9444900
X-RAY DIFFRACTIONr_mcbond_other1.4762.9444900
X-RAY DIFFRACTIONr_mcangle_it2.3765.2976111
X-RAY DIFFRACTIONr_mcangle_other2.3765.2986112
X-RAY DIFFRACTIONr_scbond_it2.073.2264958
X-RAY DIFFRACTIONr_scbond_other2.0673.2244955
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4695.8227229
X-RAY DIFFRACTIONr_long_range_B_refined4.68529.310780
X-RAY DIFFRACTIONr_long_range_B_other4.68529.3210749
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.458 Å
RfactorNum. reflection% reflection
Rfree0.371 193 -
Rwork0.304 3620 -
obs--96.41 %

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