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- PDB-6hfd: Human dihydroorotase mutant F1563L apo structure -

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Basic information

Entry
Database: PDB / ID: 6hfd
TitleHuman dihydroorotase mutant F1563L apo structure
ComponentsCAD protein
KeywordsBIOSYNTHETIC PROTEIN / de novo pyrimidine biosynthesis / CAD / TIM-barrel / carboxylated lysine
Function / homology
Function and homology information


aspartate binding / response to cortisol / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / dihydroorotase / citrulline biosynthetic process / aspartate carbamoyltransferase / glutaminase ...aspartate binding / response to cortisol / carbamoyl-phosphate synthase (glutamine-hydrolysing) / carbamoyl-phosphate synthase (ammonia) / carbamoyl-phosphate synthase (ammonia) activity / carbamoyl-phosphate synthase (glutamine-hydrolyzing) activity / dihydroorotase / citrulline biosynthetic process / aspartate carbamoyltransferase / glutaminase / aspartate carbamoyltransferase activity / dihydroorotase activity / Pyrimidine biosynthesis / UDP biosynthetic process / glutaminase activity / UTP biosynthetic process / glutamine metabolic 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 / cellular response to epidermal growth factor stimulus / xenobiotic metabolic process / liver development / cell projection / female pregnancy / peptidyl-threonine phosphorylation / 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: 1.86996804092 Å
AuthorsRamon-Maiques, S. / Grande Garcia, A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2016-80570-R Spain
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Characterization of the catalytic flexible loop in the dihydroorotase domain of the human multi-enzymatic protein CAD.
Authors: Del Cano-Ochoa, F. / Grande-Garcia, A. / Reverte-Lopez, M. / D'Abramo, M. / Ramon-Maiques, S.
History
DepositionAug 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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.conn_type_id / _struct_conn.id / _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_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_conn_type.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)43,3149
Polymers42,8681
Non-polymers4468
Water4,756264
1
A: CAD protein
hetero molecules

A: CAD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,62718
Polymers85,7362
Non-polymers89116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area4770 Å2
ΔGint-323 kcal/mol
Surface area25100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.560, 158.770, 60.890
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-2236-

HOH

21A-2251-

HOH

31A-2253-

HOH

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Components

#1: Protein CAD protein


Mass: 42867.977 Da / Num. of mol.: 1 / Mutation: F1563L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAD / Plasmid: pOPIN-M / Cell line (production host): HEK293 GnTI / Production host: Homo sapiens (human)
References: UniProt: P27708, carbamoyl-phosphate synthase (glutamine-hydrolysing), aspartate carbamoyltransferase, dihydroorotase
#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.: 264 / 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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Protein at 2-3 mg/ml in 20 mM Tris pH 8, 0.15 M NaCl, 0.02 mM zinc sulfate, 0.2 mM TCEP Mother liquor: 2.5-3 M potassium formate, 0.1 M HEPES pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.85→72.55 Å / Num. obs: 62727 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 23.5504275189 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.089 / Net I/σ(I): 17.8
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 3.8 / Num. unique obs: 2507 / CC1/2: 0.913 / Rrim(I) all: 0.686 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4c6c

4c6c


Resolution: 1.86996804092→39.6925 Å / SU ML: 0.145429233573 / Cross valid method: FREE R-VALUE / σ(F): 1.12407366769 / Phase error: 15.2778659353
RfactorNum. reflection% reflection
Rfree0.166984821771 3124 4.9803115086 %
Rwork0.131838839032 --
obs0.133602038053 62727 99.289287071 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 32.2001666768 Å2
Refinement stepCycle: LAST / Resolution: 1.86996804092→39.6925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2785 0 16 266 3067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004577060780752979
X-RAY DIFFRACTIONf_angle_d0.8902308287184079
X-RAY DIFFRACTIONf_chiral_restr0.139782094912459
X-RAY DIFFRACTIONf_plane_restr0.005053401259539
X-RAY DIFFRACTIONf_dihedral_angle_d21.65013494881817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.89920.2664003762831440.2187159719082753X-RAY DIFFRACTION99.1783635741
1.8992-1.93030.2002884500921390.1939160984742673X-RAY DIFFRACTION99.4342291372
1.9303-1.96360.1937419056251480.1692133821622735X-RAY DIFFRACTION99.1403026135
1.9636-1.99930.2170074784721360.1600157802732687X-RAY DIFFRACTION98.9484752892
1.9993-2.03780.1961483913641370.1546717253042735X-RAY DIFFRACTION99.6184530003
2.0378-2.07940.1767156105591430.1338344798422702X-RAY DIFFRACTION99.7545582048
2.0794-2.12460.1901172161371420.1188715439412740X-RAY DIFFRACTION99.7577016269
2.1246-2.1740.1731327461440.1169254039142697X-RAY DIFFRACTION99.789251844
2.174-2.22830.1366937982691470.1119992920732708X-RAY DIFFRACTION99.7205728257
2.2283-2.28860.1510710443731450.111657420852746X-RAY DIFFRACTION99.8618307427
2.2886-2.35590.1429836407251460.1048149450032718X-RAY DIFFRACTION99.721448468
2.3559-2.4320.1626918824831400.107313021442720X-RAY DIFFRACTION99.7558423439
2.432-2.51890.1168771716881390.1105791931932711X-RAY DIFFRACTION99.7549877494
2.5189-2.61970.1457631390431420.1167023416862716X-RAY DIFFRACTION99.7556719023
2.6197-2.73890.1590043637991380.1237127518972703X-RAY DIFFRACTION99.1623036649
2.7389-2.88330.173256381871460.13410428382727X-RAY DIFFRACTION99.6877168633
2.8833-3.06380.1947784792251420.1297239073132709X-RAY DIFFRACTION99.5460893855
3.0638-3.30030.172820400021420.1234957189542700X-RAY DIFFRACTION99.2318435754
3.3003-3.63220.1627036936091420.1230360728172702X-RAY DIFFRACTION99.1286162426
3.6322-4.15730.1511631716721420.1164855583322701X-RAY DIFFRACTION98.7838776928
4.1573-5.23590.142978018921420.118975063522649X-RAY DIFFRACTION97.5192173305
5.2359-39.70140.198115787591380.1883503384142671X-RAY DIFFRACTION97.2645429363

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