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- PDB-7t5y: E. coli dihydroorotate dehydrogenase bound to the inhibitor HMNQ -

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Basic information

Entry
Database: PDB / ID: 7t5y
TitleE. coli dihydroorotate dehydrogenase bound to the inhibitor HMNQ
ComponentsDihydroorotate dehydrogenase (quinone)Dihydroorotate dehydrogenase (quinone)
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / inhibitor / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


pyrimidine ribonucleotide biosynthetic process / dihydroorotate dehydrogenase (quinone) activity / dihydroorotate dehydrogenase (quinone) / dihydroorotate dehydrogenase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / FMN binding / membrane / plasma membrane / cytosol
Similarity search - Function
Dihydroorotate dehydrogenase, class 1/ 2 / Dihydroorotate dehydrogenase, class 2 / Dihydroorotate dehydrogenase signature 1. / Dihydroorotate dehydrogenase signature 2. / Dihydroorotate dehydrogenase, conserved site / Dihydroorotate dehydrogenase domain / Dihydroorotate dehydrogenase / Aldolase-type TIM barrel
Similarity search - Domain/homology
3-methyl-2-[(2E)-non-2-en-1-yl]quinolin-4(1H)-one / FLAVIN MONONUCLEOTIDE / OROTIC ACID / PHOSPHATE ION / Dihydroorotate dehydrogenase (quinone)
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR / Resolution: 2.62 Å
AuthorsHorwitz, S.M. / Ambarian, J.A. / Davis, K.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Rsc Chem Biol / Year: 2022
Title: Structural insights into inhibition of the drug target dihydroorotate dehydrogenase by bacterial hydroxyalkylquinolines.
Authors: Horwitz, S.M. / Blue, T.C. / Ambarian, J.A. / Hoshino, S. / Seyedsayamdost, M.R. / Davis, K.M.
History
DepositionDec 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydroorotate dehydrogenase (quinone)
B: Dihydroorotate dehydrogenase (quinone)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4579
Polymers80,5712
Non-polymers1,8877
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-14 kcal/mol
Surface area24490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.046, 169.328, 129.970
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 40285.258 Da / Num. of mol.: 2 / Mutation: 0
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: pyrD, b0945, JW0928 / Plasmid: pET28a(+) / Details (production host): Kanamycin resistant / Production host: Escherichia coli B (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0A7E1, dihydroorotate dehydrogenase (quinone)

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Non-polymers , 5 types, 89 molecules

#2: Chemical ChemComp-F2D / 3-methyl-2-[(2E)-non-2-en-1-yl]quinolin-4(1H)-one


Mass: 283.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H25NO / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-ORO / OROTIC ACID / Orotic acid


Mass: 156.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H4N2O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.55 Å3/Da / Density % sol: 65.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1 / Details: sodium malonate, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03384 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 17, 2021
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03384 Å / Relative weight: 1
ReflectionResolution: 2.62→48.3 Å / Num. obs: 34399 / % possible obs: 99.08 % / Redundancy: 7.4 % / Biso Wilson estimate: 66.39 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.1733 / Rpim(I) all: 0.06726 / Rrim(I) all: 0.1862 / Net I/σ(I): 9.91
Reflection shellResolution: 2.625→2.719 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 0.88 / Num. unique obs: 3231 / CC1/2: 0.996 / % possible all: 93.39

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Cootmodel building
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SIR
Starting model: 7T5K

7t5k


Resolution: 2.62→48.3 Å / SU ML: 0.3676 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.0499
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2388 1259 3.66 %
Rwork0.2121 33094 -
obs0.2131 34353 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.26 Å2
Refinement stepCycle: LAST / Resolution: 2.62→48.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5039 0 130 82 5251
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115263
X-RAY DIFFRACTIONf_angle_d1.1367149
X-RAY DIFFRACTIONf_chiral_restr0.0699812
X-RAY DIFFRACTIONf_plane_restr0.0072926
X-RAY DIFFRACTIONf_dihedral_angle_d17.02181931
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.730.34731370.33073461X-RAY DIFFRACTION94.02
2.73-2.850.32311320.29863628X-RAY DIFFRACTION99.39
2.85-30.34711370.28463667X-RAY DIFFRACTION100
3-3.190.33111420.26833689X-RAY DIFFRACTION99.97
3.19-3.440.24811300.22013682X-RAY DIFFRACTION99.9
3.44-3.790.25311460.21463690X-RAY DIFFRACTION100
3.79-4.330.22071390.18213699X-RAY DIFFRACTION99.25
4.33-5.460.20341470.17173721X-RAY DIFFRACTION99.92
5.46-48.30.19691490.20673857X-RAY DIFFRACTION99.45

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