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- PDB-4c6q: Crystal structure of the dihydroorotase domain of human CAD C1613... -

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Basic information

Entry
Database: PDB / ID: 4c6q
TitleCrystal structure of the dihydroorotase domain of human CAD C1613S mutant bound to substrate at pH 7.0
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 / OROTIC ACID / Multifunctional protein CAD
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.659 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 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 / 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 / _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_alt_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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

Downloads & links

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Assembly

Deposited unit
A: CAD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5479
Polymers42,9001
Non-polymers6478
Water7,764431
1
A: CAD PROTEIN
hetero molecules

A: CAD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,09418
Polymers85,8002
Non-polymers1,29416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5020 Å2
ΔGint-184.7 kcal/mol
Surface area25890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.070, 158.653, 61.661
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-2829-

FMT

21A-2829-

FMT

31A-2036-

HOH

41A-2078-

HOH

51A-2267-

HOH

61A-2360-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein CAD PROTEIN / DIHYDROOROTASE


Mass: 42899.953 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) / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: P27708, dihydroorotase

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Non-polymers , 5 types, 439 molecules

#2: Chemical ChemComp-ORO / OROTIC ACID


Mass: 156.096 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H4N2O4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NCD / N-CARBAMOYL-L-ASPARTATE


Mass: 176.127 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H8N2O5
#5: Chemical
ChemComp-FMT / FORMIC ACID


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


Mass: 18.015 Da / Num. of mol.: 431 / 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 7.0

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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: May 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→47.08 Å / Num. obs: 47725 / % possible obs: 97.4 % / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.5
Reflection shellResolution: 1.66→1.7 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.1 / % possible all: 96.2

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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: 1.659→47.077 Å / SU ML: 0.17 / σ(F): 1.18 / Phase error: 16.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1628 4499 5 %
Rwork0.1174 --
obs0.1197 47725 97.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.659→47.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2795 0 37 431 3263
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133136
X-RAY DIFFRACTIONf_angle_d1.3124321
X-RAY DIFFRACTIONf_dihedral_angle_d14.6831191
X-RAY DIFFRACTIONf_chiral_restr0.084485
X-RAY DIFFRACTIONf_plane_restr0.006570
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.659-1.67790.28961410.20482701X-RAY DIFFRACTION93
1.6779-1.69760.25871500.20162871X-RAY DIFFRACTION99
1.6976-1.71830.24821530.18952919X-RAY DIFFRACTION99
1.7183-1.74010.26711530.17512829X-RAY DIFFRACTION98
1.7401-1.7630.21861500.16222846X-RAY DIFFRACTION98
1.763-1.78710.23751490.16422909X-RAY DIFFRACTION98
1.7871-1.81260.22641490.15592799X-RAY DIFFRACTION96
1.8126-1.83970.22631460.15312711X-RAY DIFFRACTION95
1.8397-1.86840.24041520.1422929X-RAY DIFFRACTION98
1.8684-1.89910.21061480.14112849X-RAY DIFFRACTION98
1.8991-1.93180.2291550.12712827X-RAY DIFFRACTION97
1.9318-1.9670.17321520.11892832X-RAY DIFFRACTION98
1.967-2.00480.16751490.11622891X-RAY DIFFRACTION98
2.0048-2.04570.17421510.10762862X-RAY DIFFRACTION98
2.0457-2.09020.14981490.11522806X-RAY DIFFRACTION97
2.0902-2.13880.16381470.09522845X-RAY DIFFRACTION97
2.1388-2.19230.14481470.08952719X-RAY DIFFRACTION94
2.1923-2.25160.161560.09182853X-RAY DIFFRACTION97
2.2516-2.31780.17641550.09552847X-RAY DIFFRACTION98
2.3178-2.39260.16961540.09592889X-RAY DIFFRACTION99
2.3926-2.47820.12311520.09182889X-RAY DIFFRACTION99
2.4782-2.57740.1591510.09482872X-RAY DIFFRACTION98
2.5774-2.69470.16991530.09952853X-RAY DIFFRACTION98
2.6947-2.83670.16971370.1132741X-RAY DIFFRACTION95
2.8367-3.01440.17111450.11422897X-RAY DIFFRACTION99
3.0144-3.24710.13581560.1132882X-RAY DIFFRACTION99
3.2471-3.57380.13831510.10392875X-RAY DIFFRACTION99
3.5738-4.09060.1171420.09622760X-RAY DIFFRACTION95
4.0906-5.15280.12391540.10172876X-RAY DIFFRACTION98
5.1528-47.09610.1631520.17372810X-RAY DIFFRACTION97

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