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- PDB-8pbm: Mutant R1789Q of the dihydroorotase domain of human CAD protein b... -

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Basic information

Entry
Database: PDB / ID: 8pbm
TitleMutant R1789Q of the dihydroorotase domain of human CAD protein bound to the substrate dihydroorotate
ComponentsCAD protein
KeywordsHYDROLASE / Nucleotide metabolism / de novo pyrimidine synthesis / CAD disease / multienzymatic protein / zinc / carboxylated lysine / BIOSYNTHETIC PROTEIN
Function / homology
Function and homology information


aspartate binding / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / dihydroorotase / citrulline biosynthetic process / response to cortisol / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity ...aspartate binding / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / dihydroorotase / citrulline biosynthetic process / response to cortisol / aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / glutaminase / dihydroorotase activity / Pyrimidine biosynthesis / glutaminase activity / UDP biosynthetic process / glutamine metabolic process / UTP biosynthetic process / response to caffeine / response to starvation / response to amine / response to testosterone / 'de novo' UMP biosynthetic process / animal organ regeneration / 'de novo' pyrimidine nucleobase biosynthetic process / lactation / xenobiotic metabolic process / cellular response to epidermal growth factor stimulus / cell projection / liver development / female pregnancy / response to insulin / nuclear matrix / terminal bouton / heart development / protein kinase activity / neuronal cell body / enzyme binding / protein-containing complex / extracellular exosome / zinc ion binding / ATP binding / identical protein binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthase large subunit, CPSase domain / Carbamoyl-phosphate synthase, small subunit / Carbamoyl-phosphate synthase, large subunit / Carbamoyl-phosphate synthase small subunit, GATase1 domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / Carbamoyl-phosphate synthase small chain, CPSase domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain ...Carbamoyl-phosphate synthase small subunit, N-terminal domain / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain / Carbamoyl-phosphate synthase large subunit, CPSase domain / Carbamoyl-phosphate synthase, small subunit / Carbamoyl-phosphate synthase, large subunit / Carbamoyl-phosphate synthase small subunit, GATase1 domain / Carbamoyl-phosphate synthase small subunit, N-terminal domain superfamily / Carbamoyl-phosphate synthetase, large subunit oligomerisation domain superfamily / Carbamoyl-phosphate synthase small chain, CPSase domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain / Carbamoyl-phosphate synthetase large chain, oligomerisation domain / Carbamoyl-phosphate synthase small chain, CPSase domain / Dihydroorotase signature 1. / Dihydroorotase signature 2. / Dihydroorotase, conserved site / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain profile. / MGS-like domain / Aspartate carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Aspartate/ornithine carbamoyltransferase / Aspartate/ornithine carbamoyltransferase, Asp/Orn-binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding / Aspartate/ornithine carbamoyltransferase superfamily / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / Glutamine amidotransferase / Glutamine amidotransferase class-I / Carbamoyl-phosphate synthase subdomain signature 1. / Glutamine amidotransferase type 1 domain profile. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / Class I glutamine amidotransferase-like / Metal-dependent hydrolase / Carbamoyl-phosphate synthase subdomain signature 2.
Similarity search - Domain/homology
Chem-DOR / FORMIC ACID / Multifunctional protein CAD
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å
Authorsdel Cano-Ochoa, F. / Ramon-Maiques, S.
Funding support Spain, 3items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2021-128468NB-I00 Spain
Other privateFundacion Ramon Areces, XX National Call
Other governmentPostdoctoral fellow of the Generalitat Valenciana (APOSTD 2021)
CitationJournal: J Inherit Metab Dis / Year: 2023
Title: Beyond genetics: Deciphering the impact of missense variants in CAD deficiency.
Authors: Del Cano-Ochoa, F. / Ng, B.G. / Rubio-Del-Campo, A. / Mahajan, S. / Wilson, M.P. / Vilar, M. / Rymen, D. / Sanchez-Pintos, P. / Kenny, J. / Ley Martos, M. / Campos, T. / Wortmann, S.B. / ...Authors: Del Cano-Ochoa, F. / Ng, B.G. / Rubio-Del-Campo, A. / Mahajan, S. / Wilson, M.P. / Vilar, M. / Rymen, D. / Sanchez-Pintos, P. / Kenny, J. / Ley Martos, M. / Campos, T. / Wortmann, S.B. / Freeze, H.H. / Ramon-Maiques, S.
History
DepositionJun 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2Nov 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CAD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,40711
Polymers39,6651
Non-polymers74210
Water7,080393
1
A: CAD protein
hetero molecules

A: CAD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,81522
Polymers79,3312
Non-polymers1,48420
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area5780 Å2
ΔGint-325 kcal/mol
Surface area25080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.926, 158.197, 61.920
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
Components on special symmetry positions
IDModelComponents
11A-2327-

HOH

21A-2380-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CAD protein


Mass: 39665.363 Da / Num. of mol.: 1 / Mutation: R1789Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAD / Plasmid: pOPIN-M-huDHO-R1789Q / Cell (production host): epithelial-like / Cell line (production host): HEK293 GnTI- / Organ (production host): Embryo / Production host: Homo sapiens (human) / Tissue (production host): Kidney
References: UniProt: P27708, carbamoyl-phosphate synthase (glutamine-hydrolysing), aspartate carbamoyltransferase, dihydroorotase

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Non-polymers , 5 types, 403 molecules

#2: Chemical ChemComp-DOR / (4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID / DIHYDROOROTIC ACID


Mass: 158.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6N2O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 393 / 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: 2.53 Å3/Da / Density % sol: 51.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100mM Tris-HCl pH7, 2.7 M sodium formate, 2 mM carbamoyl aspartate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.28→79.1 Å / Num. obs: 103657 / % possible obs: 99.93 % / Redundancy: 6.5 % / Biso Wilson estimate: 14.84 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.68
Reflection shellResolution: 1.28→1.326 Å / Mean I/σ(I) obs: 2.42 / Num. unique obs: 10261 / CC1/2: 0.869

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Processing

Software
NameVersionClassification
EDNAdata collection
autoPROCdata processing
PHASERv8.0phasing
REFMACv8.0refinement
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.28→79.1 Å / SU ML: 0.1161 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.5518
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1514 5102 4.92 %
Rwork0.1283 98555 -
obs0.1294 103657 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.25 Å2
Refinement stepCycle: LAST / Resolution: 1.28→79.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2750 0 36 393 3179
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00983043
X-RAY DIFFRACTIONf_angle_d1.12574185
X-RAY DIFFRACTIONf_chiral_restr0.09478
X-RAY DIFFRACTIONf_plane_restr0.0109552
X-RAY DIFFRACTIONf_dihedral_angle_d7.3728440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.28-1.290.27821880.25063250X-RAY DIFFRACTION99.91
1.29-1.310.26251830.22993235X-RAY DIFFRACTION99.91
1.31-1.320.26172070.21583194X-RAY DIFFRACTION99.94
1.32-1.340.24891840.21053244X-RAY DIFFRACTION99.85
1.34-1.360.21551580.18643241X-RAY DIFFRACTION99.97
1.36-1.380.21121860.18133251X-RAY DIFFRACTION99.97
1.38-1.40.19631750.15993243X-RAY DIFFRACTION99.85
1.4-1.420.18911600.15283258X-RAY DIFFRACTION99.91
1.42-1.440.19561720.15253300X-RAY DIFFRACTION99.91
1.44-1.460.19071700.14373249X-RAY DIFFRACTION99.91
1.46-1.490.17361780.13353238X-RAY DIFFRACTION99.91
1.49-1.520.13241670.12573242X-RAY DIFFRACTION99.91
1.52-1.550.13281320.10913325X-RAY DIFFRACTION100
1.55-1.580.14771560.10423267X-RAY DIFFRACTION99.97
1.58-1.610.15571680.10033247X-RAY DIFFRACTION100
1.61-1.650.14971580.09893320X-RAY DIFFRACTION99.94
1.65-1.690.14721700.09373261X-RAY DIFFRACTION100
1.69-1.740.15071620.09623272X-RAY DIFFRACTION99.97
1.74-1.790.1191590.10193298X-RAY DIFFRACTION99.97
1.79-1.840.13741740.1073273X-RAY DIFFRACTION100
1.84-1.910.15241990.1083258X-RAY DIFFRACTION99.97
1.91-1.990.13111710.10323275X-RAY DIFFRACTION100
1.99-2.080.1481600.10513304X-RAY DIFFRACTION99.94
2.08-2.190.11431520.09843309X-RAY DIFFRACTION99.97
2.19-2.320.12511530.10683328X-RAY DIFFRACTION99.91
2.32-2.50.13271620.11423318X-RAY DIFFRACTION99.86
2.5-2.760.14771650.13133324X-RAY DIFFRACTION99.83
2.76-3.150.16321730.14153354X-RAY DIFFRACTION99.89
3.16-3.970.1481840.12833360X-RAY DIFFRACTION100
3.98-79.10.14581760.15373517X-RAY DIFFRACTION99.73

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