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- PDB-8pbj: Mutant R1722W of the dihydroorotase domain of human CAD protein b... -

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Basic information

Entry
Database: PDB / ID: 8pbj
TitleMutant R1722W of the dihydroorotase domain of human CAD protein bound to the substrate carbamoyl aspartate
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 / N-CARBAMOYL-L-ASPARTATE / Multifunctional protein CAD
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 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)40,46411
Polymers39,7231
Non-polymers74110
Water6,666370
1
A: CAD protein
hetero molecules

A: CAD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,92822
Polymers79,4472
Non-polymers1,48120
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area5870 Å2
ΔGint-267 kcal/mol
Surface area25130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.219, 158.537, 61.991
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-1902-

FMT

21A-2313-

HOH

31A-2329-

HOH

41A-2350-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CAD protein


Mass: 39723.445 Da / Num. of mol.: 1 / Mutation: R1722W
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): HEK293S 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, 380 molecules

#2: Chemical ChemComp-NCD / N-CARBAMOYL-L-ASPARTATE


Mass: 176.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.54 Å3/Da / Density % sol: 51.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM Tris-HCl, 2.5 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: ESRF / Beamline: ID23-2 / Wavelength: 0.87313 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Sep 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87313 Å / Relative weight: 1
ReflectionResolution: 1.55→47.25 Å / Num. obs: 260707 / % possible obs: 98.23 % / Redundancy: 6.7 % / Biso Wilson estimate: 15.67 Å2 / CC1/2: 0.997 / Net I/σ(I): 10.18
Reflection shellResolution: 1.55→1.605 Å / Mean I/σ(I) obs: 2.39 / Num. unique obs: 25487 / CC1/2: 0.784

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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: 1.55→47.25 Å / SU ML: 0.1518 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.7368
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.172 2840 4.86 %
Rwork0.1374 55544 -
obs0.139 58384 98.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.35 Å2
Refinement stepCycle: LAST / Resolution: 1.55→47.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2739 0 39 370 3148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912908
X-RAY DIFFRACTIONf_angle_d1.08833980
X-RAY DIFFRACTIONf_chiral_restr0.0605451
X-RAY DIFFRACTIONf_plane_restr0.0102523
X-RAY DIFFRACTIONf_dihedral_angle_d8.0307409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.25181740.2052729X-RAY DIFFRACTION99.04
1.57-1.60.21671370.19052775X-RAY DIFFRACTION99.35
1.6-1.630.24091510.17972773X-RAY DIFFRACTION99.15
1.63-1.670.23031530.16912765X-RAY DIFFRACTION99.18
1.67-1.70.21321510.16542754X-RAY DIFFRACTION99.28
1.7-1.740.25271610.16162760X-RAY DIFFRACTION99.25
1.74-1.790.19021440.15592781X-RAY DIFFRACTION99.19
1.79-1.830.19281300.14612785X-RAY DIFFRACTION98.95
1.83-1.890.18221290.13392769X-RAY DIFFRACTION98.64
1.89-1.950.18481490.13422777X-RAY DIFFRACTION98.65
1.95-2.020.17711300.13482777X-RAY DIFFRACTION98.44
2.02-2.10.18141600.13132761X-RAY DIFFRACTION98.72
2.1-2.20.14361470.1172758X-RAY DIFFRACTION98.44
2.2-2.310.1481320.11212790X-RAY DIFFRACTION98.15
2.31-2.460.16091310.1122788X-RAY DIFFRACTION98.08
2.46-2.650.16361260.12282797X-RAY DIFFRACTION97.89
2.65-2.910.16621290.13522772X-RAY DIFFRACTION97.32
2.91-3.330.17481390.14062788X-RAY DIFFRACTION96.98
3.33-4.20.14531310.12262788X-RAY DIFFRACTION96.02
4.2-100.15311360.15362857X-RAY DIFFRACTION94.33

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