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

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Basic information

Entry
Database: PDB / ID: 9vpt
TitleCrystal structure of the C131A mutant of Trypanosoma brucei DHODH in FMN-oxidized, dihydroorotate-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
Chem-DOR / FLAVIN MONONUCLEOTIDE / MALONATE ION / Dihydroorotate dehydrogenase (fumarate)
Similarity search - Component
Biological speciesTrypanosoma brucei brucei TREU927 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKubota, T. / Yamasaki, T. / 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
Revision 1.1Dec 10, 2025Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)141,65326
Polymers137,7664
Non-polymers3,88622
Water12,304683
1
A: Dihydroorotate dehydrogenase (fumarate)
B: Dihydroorotate dehydrogenase (fumarate)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,82613
Polymers68,8832
Non-polymers1,94311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8750 Å2
ΔGint-12 kcal/mol
Surface area21010 Å2
MethodPISA
2
C: Dihydroorotate dehydrogenase (fumarate)
D: Dihydroorotate dehydrogenase (fumarate)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,82613
Polymers68,8832
Non-polymers1,94311
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-13 kcal/mol
Surface area21140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.120, 146.655, 66.287
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-552-

HOH

21A-639-

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-DOR / (4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID / DIHYDROOROTIC ACID


Mass: 158.112 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C5H6N2O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 683 / 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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 1.5 M malonate, 0.1 M citrate, 10 mM L-dihydroorotate. soaked into 50 mM L-dihydroorotate (15 min).

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 108205 / % possible obs: 99.9 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 16.33
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.731 / Num. unique obs: 4893

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XFV

5xfv


Resolution: 1.9→49.17 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.584 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20165 5413 5 %RANDOM
Rwork0.18282 ---
obs0.18378 102832 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.795 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.9→49.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9573 0 266 683 10522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01210094
X-RAY DIFFRACTIONr_bond_other_d0.0010.0169552
X-RAY DIFFRACTIONr_angle_refined_deg1.0251.82313683
X-RAY DIFFRACTIONr_angle_other_deg0.41.73122094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.451262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.019556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.718101664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0540.21511
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211672
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022172
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_it0.5112.4995030
X-RAY DIFFRACTIONr_mcbond_other0.5112.4995030
X-RAY DIFFRACTIONr_mcangle_it0.934.5026286
X-RAY DIFFRACTIONr_mcangle_other0.934.5026287
X-RAY DIFFRACTIONr_scbond_it0.5082.5785064
X-RAY DIFFRACTIONr_scbond_other0.5082.5775061
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9114.7267394
X-RAY DIFFRACTIONr_long_range_B_refined2.30625.7711236
X-RAY DIFFRACTIONr_long_range_B_other2.16924.9511102
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 397 -
Rwork0.282 7536 -
obs--100 %

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