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- PDB-8pbr: Mutant R1475Q of the dihydroorotase domain of human CAD protein i... -

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Basic information

Entry
Database: PDB / ID: 8pbr
TitleMutant R1475Q of the dihydroorotase domain of human CAD protein in apo form
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
FORMIC ACID / Multifunctional protein CAD
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 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 Spain
Other governmentPostdoctoral fellow of the Generalitat Valenciana (APOSTD 2021) Spain
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

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Assembly

Deposited unit
A: CAD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1178
Polymers39,7361
Non-polymers3807
Water2,954164
1
A: CAD protein
hetero molecules

A: CAD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,23416
Polymers79,4732
Non-polymers76114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Unit cell
Length a, b, c (Å)81.738, 159.318, 61.031
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

#1: Protein CAD protein


Mass: 39736.441 Da / Num. of mol.: 1 / Mutation: R1475Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAD / Plasmid: pOPIN-M-huDHO-R1475Q / 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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: Zn
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.48 Å3/Da / Density % sol: 50.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 100 mM HEPES pH 7.0, 2.6 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 22, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.05→48.45 Å / Num. obs: 23812 / % possible obs: 94.26 % / Redundancy: 6.4 % / Biso Wilson estimate: 30.99 Å2 / CC1/2: 0.998 / Net I/σ(I): 14.24
Reflection shellResolution: 2.056→2.129 Å / Mean I/σ(I) obs: 2.32 / Num. unique obs: 1777 / CC1/2: 0.82

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Processing

Software
NameVersionClassification
EDNAdata collection
XDSdata reduction
PHASERv8.0phasing
REFMACv8.0refinement
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.06→48.45 Å / SU ML: 0.221 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.0272
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2205 1150 4.83 %
Rwork0.1675 22655 -
obs0.1701 23805 94.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.82 Å2
Refinement stepCycle: LAST / Resolution: 2.06→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2734 0 15 164 2913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032882
X-RAY DIFFRACTIONf_angle_d0.61833947
X-RAY DIFFRACTIONf_chiral_restr0.0427452
X-RAY DIFFRACTIONf_plane_restr0.004517
X-RAY DIFFRACTIONf_dihedral_angle_d6.6399405
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.06-2.150.31391090.21392266X-RAY DIFFRACTION76.51
2.15-2.260.26591220.19882460X-RAY DIFFRACTION82.47
2.26-2.40.27491510.19512954X-RAY DIFFRACTION99.97
2.4-2.590.23871500.17682959X-RAY DIFFRACTION99.94
2.59-2.850.22051570.1732874X-RAY DIFFRACTION96.53
2.85-3.260.23491350.17863008X-RAY DIFFRACTION99.97
3.26-4.110.19371650.14742987X-RAY DIFFRACTION98.53
4.11-48.450.20121610.15583147X-RAY DIFFRACTION99.73

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