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- PDB-6hfe: Human dihydroorotase mutant F1563T apo structure -

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Basic information

Entry
Database: PDB / ID: 6hfe
TitleHuman dihydroorotase mutant F1563T 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 / response to caffeine / response to testosterone / response to starvation / glutamine metabolic process / response to amine / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / animal organ regeneration / cellular response to epidermal growth factor stimulus / lactation / 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 / membrane / identical protein binding / nucleus / 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 / MGS-like domain profile. / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain / Aspartate carbamoyltransferase / Aspartate and ornithine carbamoyltransferases signature. / Glutamine amidotransferase class-I / Glutamine amidotransferase / 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 / 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 hydrolases / 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: 1.47997437573 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)43,40811
Polymers42,8701
Non-polymers53810
Water6,269348
1
A: CAD protein
hetero molecules

A: CAD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,81522
Polymers85,7402
Non-polymers1,07620
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area5260 Å2
ΔGint-323 kcal/mol
Surface area25760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.700, 158.730, 60.960
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-1905-

FMT

21A-2291-

HOH

31A-2319-

HOH

41A-2323-

HOH

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Components

#1: Protein CAD protein /


Mass: 42869.949 Da / Num. of mol.: 1 / Mutation: F1563T
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 / Formic acid


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


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.5 Å3/Da / Density % sol: 50.72 %
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 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.47997437573→72.64 Å / Num. obs: 66300 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 17.6622678116 Å2 / CC1/2: 0.919 / Rrim(I) all: 0.059 / Net I/σ(I): 17.9
Reflection shellResolution: 1.47997437573→1.52 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 3 / Num. unique obs: 4859 / CC1/2: 0.885 / Rrim(I) all: 0.677 / % 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: 1.47997437573→30.48 Å / SU ML: 0.122215176541 / Cross valid method: FREE R-VALUE / σ(F): 1.08840149591 / Phase error: 14.3565032789
RfactorNum. reflection% reflection
Rfree0.15756945324 6344 4.98738217467 %
Rwork0.125562628275 --
obs0.127170477263 66283 99.5998809822 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.5601612268 Å2
Refinement stepCycle: LAST / Resolution: 1.47997437573→30.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2784 0 22 350 3156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005295465566552983
X-RAY DIFFRACTIONf_angle_d0.9577366179864077
X-RAY DIFFRACTIONf_chiral_restr0.154906677306455
X-RAY DIFFRACTIONf_plane_restr0.00568499734839541
X-RAY DIFFRACTIONf_dihedral_angle_d26.12531602781109
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.49680.2912594780642130.237624339734029X-RAY DIFFRACTION99.6242367309
1.4968-1.51440.2407134111742130.2038129092344027X-RAY DIFFRACTION99.8116760829
1.5144-1.53290.2330340531992030.1910838913474010X-RAY DIFFRACTION99.6452223273
1.5329-1.55230.2378041601992150.1787463913164049X-RAY DIFFRACTION99.8594847775
1.5523-1.57270.1954672481872150.1712367030634049X-RAY DIFFRACTION99.6960486322
1.5727-1.59420.1846655339792080.1618936625134037X-RAY DIFFRACTION99.7649823737
1.5942-1.6170.1947720180332120.162688686464019X-RAY DIFFRACTION99.5529411765
1.617-1.64110.2061923743792120.1536731875734057X-RAY DIFFRACTION99.5801259622
1.6411-1.66680.1809720926642050.1435748936444006X-RAY DIFFRACTION99.7158418186
1.6668-1.69410.1628763483792150.1356563162164042X-RAY DIFFRACTION99.6488764045
1.6941-1.72330.1626441672052130.132361879474012X-RAY DIFFRACTION99.6932515337
1.7233-1.75470.1540283281842130.1222327536094043X-RAY DIFFRACTION99.7889800703
1.7547-1.78840.1675777402212170.1194114881754033X-RAY DIFFRACTION99.8824911868
1.7884-1.82490.1591863149442130.1136945621654041X-RAY DIFFRACTION99.8826015497
1.8249-1.86460.1497376324022140.1115090766614067X-RAY DIFFRACTION99.8600419874
1.8646-1.90790.1502901912792140.1105967477313989X-RAY DIFFRACTION99.668010434
1.9079-1.95570.142862698062120.1117130140924042X-RAY DIFFRACTION99.8357193147
1.9557-2.00850.140531710442070.1088674453184017X-RAY DIFFRACTION99.8109640832
2.0085-2.06760.1344050421782130.1058425234814056X-RAY DIFFRACTION99.6964035497
2.0676-2.13430.1272551509352120.09786077315754014X-RAY DIFFRACTION99.6698113208
2.1343-2.21060.1569048799832140.09662061349734037X-RAY DIFFRACTION99.3224299065
2.2106-2.29910.1476579366182100.09864042980564036X-RAY DIFFRACTION99.6245893947
2.2991-2.40370.1170260510942160.1037781664064044X-RAY DIFFRACTION99.7191011236
2.4037-2.53030.1309821753412110.1117233814653996X-RAY DIFFRACTION99.7392128971
2.5303-2.68880.193298354762040.1210335985574053X-RAY DIFFRACTION99.4161606726
2.6888-2.89620.1611112045652060.1337550072333996X-RAY DIFFRACTION99.1973559962
2.8962-3.18740.1660553694412170.133657445214041X-RAY DIFFRACTION99.3467102193
3.1874-3.6480.1522316652632060.1216264774783986X-RAY DIFFRACTION99.0314197968
3.648-4.59350.1339641132792130.1102726003694018X-RAY DIFFRACTION99.2959399202
4.5935-30.48650.1771993548062080.1587867034994011X-RAY DIFFRACTION98.6900584795

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