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- PDB-4c6c: Crystal structure of the dihydroorotase domain of human CAD in ap... -

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Basic information

Entry
Database: PDB / ID: 4c6c
TitleCrystal structure of the dihydroorotase domain of human CAD in apo- form obtained recombinantly from HEK293 cells.
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) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / dihydroorotase / response to cortisol / citrulline biosynthetic process / aspartate carbamoyltransferase / glutaminase ...aspartate binding / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / dihydroorotase / response to cortisol / citrulline biosynthetic process / aspartate carbamoyltransferase / glutaminase / aspartate carbamoyltransferase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / glutaminase activity / 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 / peptidyl-threonine phosphorylation / xenobiotic metabolic process / cellular response to epidermal growth factor stimulus / liver development / cell projection / female pregnancy / response to insulin / terminal bouton / nuclear matrix / heart development / protein autophosphorylation / protein kinase activity / neuronal cell body / enzyme binding / protein-containing complex / extracellular exosome / zinc ion binding / ATP binding / identical protein binding / nucleus / membrane / cytosol / cytoplasm
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 / Glutamine amidotransferase type 1 domain profile. / Carbamoyl-phosphate synthase subdomain signature 1. / 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 / Multifunctional protein CAD
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.451 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 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _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_asym_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.ptnr1_symmetry / _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_asym_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: CAD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3629
Polymers42,9161
Non-polymers4468
Water6,756375
1
A: CAD PROTEIN
hetero molecules

A: CAD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,72418
Polymers85,8322
Non-polymers89116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3640 Å2
ΔGint-296.8 kcal/mol
Surface area26650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.110, 158.800, 60.760
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-2827-

FMT

21A-2827-

FMT

31A-2025-

HOH

41A-2055-

HOH

51A-2193-

HOH

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Components

#1: Protein CAD PROTEIN / DIHYDROOROTASE


Mass: 42916.020 Da / Num. of mol.: 1 / Fragment: RESIDUES 1456-1846
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: P27708, EC: 3.4.2.3
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / 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.: 375 / 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: 7 / Details: pH 7

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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: Dec 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→48.25 Å / Num. obs: 69725 / % possible obs: 99 % / Observed criterion σ(I): 1 / Redundancy: 9.5 % / Biso Wilson estimate: 13.56 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.2
Reflection shellResolution: 1.45→1.49 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 3.2 / % possible all: 90.6

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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 4BY3

4by3


Resolution: 1.451→41.055 Å / SU ML: 0.08 / σ(F): 2 / Phase error: 12.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1478 3487 5 %
Rwork0.1225 --
obs0.1238 69725 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.451→41.055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2769 0 16 375 3160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013049
X-RAY DIFFRACTIONf_angle_d1.3364195
X-RAY DIFFRACTIONf_dihedral_angle_d14.3311169
X-RAY DIFFRACTIONf_chiral_restr0.083473
X-RAY DIFFRACTIONf_plane_restr0.007551
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4514-1.47130.23611240.18172339X-RAY DIFFRACTION88
1.4713-1.49230.18491300.15582470X-RAY DIFFRACTION93
1.4923-1.51460.17261330.1342533X-RAY DIFFRACTION96
1.5146-1.53820.14341380.12692620X-RAY DIFFRACTION99
1.5382-1.56350.16211390.11112644X-RAY DIFFRACTION100
1.5635-1.59040.14271400.10172656X-RAY DIFFRACTION100
1.5904-1.61930.1341390.10022634X-RAY DIFFRACTION100
1.6193-1.65050.14871400.09372658X-RAY DIFFRACTION100
1.6505-1.68420.14071400.0962659X-RAY DIFFRACTION100
1.6842-1.72080.12331390.0892652X-RAY DIFFRACTION100
1.7208-1.76080.11921390.08582647X-RAY DIFFRACTION100
1.7608-1.80490.13261410.08972663X-RAY DIFFRACTION100
1.8049-1.85370.1091390.09112646X-RAY DIFFRACTION100
1.8537-1.90820.12961410.09482681X-RAY DIFFRACTION100
1.9082-1.96980.1241400.09752657X-RAY DIFFRACTION100
1.9698-2.04020.14341410.10192689X-RAY DIFFRACTION100
2.0402-2.12190.11771400.09872661X-RAY DIFFRACTION100
2.1219-2.21840.12021410.1012679X-RAY DIFFRACTION100
2.2184-2.33540.14961410.10962678X-RAY DIFFRACTION100
2.3354-2.48170.14481410.11362680X-RAY DIFFRACTION100
2.4817-2.67330.1521420.12432683X-RAY DIFFRACTION100
2.6733-2.94220.16621420.1422711X-RAY DIFFRACTION100
2.9422-3.36780.1481440.13962723X-RAY DIFFRACTION100
3.3678-4.24240.15241440.12592741X-RAY DIFFRACTION100
4.2424-41.07140.17581490.17132834X-RAY DIFFRACTION99

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