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- PDB-4c6n: Crystal structure of the dihydroorotase domain of human CAD E1637... -

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Basic information

Entry
Database: PDB / ID: 4c6n
TitleCrystal structure of the dihydroorotase domain of human CAD E1637T mutant bound to substrate at pH 6.0
ComponentsCAD PROTEIN
KeywordsHYDROLASE / DE NOVO PYRIMIDINE BIOSYNTHESIS / AMIDOHYDROLASE SUPERFAMILY / METALLOENZYME / ZINC BINDING / HISTIDINATE ANION
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. / Metal-dependent hydrolases / Class I glutamine amidotransferase-like / Metal-dependent hydrolase / Carbamoyl-phosphate synthase subdomain signature 2. / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
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: 1.899 Å
AuthorsRamon-Maiques, S. / Lallous, N. / Grande-Garcia, A.
CitationJournal: Structure / Year: 2014
Title: Structure, Functional Characterization and Evolution of the Dihydroorotase Domain of Human Cad.
Authors: Grande-Garcia, A. / Lallous, N. / Diaz-Tejada, C. / Ramon-Maiques, S.
History
DepositionSep 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)43,3337
Polymers42,8881
Non-polymers4456
Water5,116284
1
A: CAD PROTEIN
hetero molecules

A: CAD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,66614
Polymers85,7762
Non-polymers89012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3930 Å2
ΔGint-191.8 kcal/mol
Surface area26130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.100, 159.170, 60.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-2828-

FMT

21A-2828-

FMT

31A-2009-

HOH

41A-2033-

HOH

51A-2034-

HOH

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Components

#1: Protein CAD PROTEIN / DIHYDROOROTASE


Mass: 42888.008 Da / Num. of mol.: 1 / Fragment: RESIDUES 1456-1846 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPIN-M / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: P27708, dihydroorotase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-NCD / N-CARBAMOYL-L-ASPARTATE


Mass: 176.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8N2O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 6 / Details: pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→48.4 Å / Num. obs: 31728 / % possible obs: 99.3 % / Observed criterion σ(I): 1 / Redundancy: 5.6 % / Biso Wilson estimate: 21.05 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.4
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 6.1 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C6C

4c6c


Resolution: 1.899→48.399 Å / SU ML: 0.11 / σ(F): 2 / Phase error: 16.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1698 1587 5 %
Rwork0.1456 --
obs0.1469 31728 99.29 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.899→48.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2791 0 23 284 3098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133028
X-RAY DIFFRACTIONf_angle_d1.1194155
X-RAY DIFFRACTIONf_dihedral_angle_d13.0771134
X-RAY DIFFRACTIONf_chiral_restr0.075466
X-RAY DIFFRACTIONf_plane_restr0.005548
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8993-1.96060.20051330.15422520X-RAY DIFFRACTION93
1.9606-2.03070.21261420.15852712X-RAY DIFFRACTION100
2.0307-2.1120.18221440.15162728X-RAY DIFFRACTION100
2.112-2.20810.19741430.1392725X-RAY DIFFRACTION100
2.2081-2.32450.16491450.14412741X-RAY DIFFRACTION100
2.3245-2.47010.1931430.15212730X-RAY DIFFRACTION100
2.4701-2.66080.2281460.15332762X-RAY DIFFRACTION100
2.6608-2.92860.20741450.16082756X-RAY DIFFRACTION100
2.9286-3.35220.1691450.14542763X-RAY DIFFRACTION100
3.3522-4.22310.14271470.12322794X-RAY DIFFRACTION100
4.2231-48.41510.12961540.15072910X-RAY DIFFRACTION99

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