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- PDB-6hfp: Human dihydroorotase mutant F1563T co-crystallized with carbamoyl... -

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Basic information

Entry
Database: PDB / ID: 6hfp
TitleHuman dihydroorotase mutant F1563T co-crystallized with carbamoyl aspartate at pH 7.0
ComponentsCAD protein
KeywordsBIOSYNTHETIC PROTEIN / de novo pyrimidine biosynthesis / CAD / TIM-barrel / carboxylated lysine
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
Chem-DOR / FORMIC ACID / Multifunctional protein CAD
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19822864429 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_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.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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_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_conn.ptnr2_symmetry / _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)43,46010
Polymers42,8561
Non-polymers6049
Water9,170509
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, Dimers detected by SEC-MALS and sedimentation velocity analysis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-133 kcal/mol
Surface area14060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.104, 158.948, 61.210
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-1907-

FMT

21A-1907-

FMT

31A-2388-

HOH

41A-2436-

HOH

51A-2464-

HOH

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Components

#1: Protein CAD protein


Mass: 42855.922 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-DOR / (4S)-2,6-DIOXOHEXAHYDROPYRIMIDINE-4-CARBOXYLIC ACID / DIHYDROOROTIC ACID


Mass: 158.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6N2O4
#4: Chemical
ChemComp-FMT / FORMIC ACID


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


Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.53 Å3/Da / Density % sol: 51.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
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 with 4 mM carbamoyl asparate. Mother liquor: 2.5-3 M potassium formate, 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.19822864429→48.4940488716 Å / Num. obs: 124981 / % possible obs: 99.6 % / Redundancy: 6.4 % / Biso Wilson estimate: 13.2304425898 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.046 / Net I/σ(I): 21.6
Reflection shellResolution: 1.19822864429→1.24 Å / Redundancy: 6.2 % / Mean I/σ(I) obs: 2.6 / Num. unique obs: 12167 / CC1/2: 0.87 / Rrim(I) all: 0.67 / % possible all: 97.8

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4c6i

4c6i


Resolution: 1.19822864429→48.4940488716 Å / SU ML: 0.0849949298931 / Cross valid method: FREE R-VALUE / σ(F): 1.33784209461 / Phase error: 13.3187374055
RfactorNum. reflection% reflection
Rfree0.1366740553 6232 4.98771479107 %
Rwork0.121748467499 --
obs0.122501989216 124947 99.641934352 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 21.0978390917 Å2
Refinement stepCycle: LAST / Resolution: 1.19822864429→48.4940488716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2780 0 27 513 3320
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01068768918683029
X-RAY DIFFRACTIONf_angle_d1.233831929534158
X-RAY DIFFRACTIONf_chiral_restr0.191102887667470
X-RAY DIFFRACTIONf_plane_restr0.00929227358199550
X-RAY DIFFRACTIONf_dihedral_angle_d25.23302557541145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1982-1.21180.2470449116852120.2316166308923690X-RAY DIFFRACTION93.9561762581
1.2118-1.22610.2260068839411990.218281538043944X-RAY DIFFRACTION99.5674116799
1.2261-1.24110.2264085587831990.1987914355793918X-RAY DIFFRACTION99.9029361805
1.2411-1.25680.1928472581161990.1817974656353913X-RAY DIFFRACTION99.8058252427
1.2568-1.27330.1988031633521860.1793329566513976X-RAY DIFFRACTION99.736400671
1.2733-1.29080.1628839614692090.1611327876143934X-RAY DIFFRACTION99.9276410999
1.2908-1.30920.1789261157171950.1589918583313921X-RAY DIFFRACTION99.8786702257
1.3092-1.32870.1678956587312310.1447111489913925X-RAY DIFFRACTION99.8798365777
1.3287-1.34950.1652772039671860.135228850163936X-RAY DIFFRACTION99.8788466198
1.3495-1.37160.1580244151712060.1309730607553952X-RAY DIFFRACTION99.7361477573
1.3716-1.39530.1393459239122040.1181140598483922X-RAY DIFFRACTION99.8789639313
1.3953-1.42070.136587839882080.1112397346623960X-RAY DIFFRACTION99.8801821232
1.4207-1.4480.1350796509381910.1082877061663948X-RAY DIFFRACTION99.8070894623
1.448-1.47750.1267058843532150.1024850038313902X-RAY DIFFRACTION99.8060606061
1.4775-1.50970.1218516526272090.09250930146293955X-RAY DIFFRACTION99.9280057595
1.5097-1.54480.1180380447931990.09349388857223986X-RAY DIFFRACTION99.8806682578
1.5448-1.58340.1096702042162270.08787426733113910X-RAY DIFFRACTION100
1.5834-1.62620.1056904273692000.08805651897073966X-RAY DIFFRACTION99.9520153551
1.6262-1.67410.1139247672212190.09052295223473957X-RAY DIFFRACTION100
1.6741-1.72810.1054789197062120.09127657450043955X-RAY DIFFRACTION99.952026865
1.7281-1.78990.1151191617752080.09342041913163971X-RAY DIFFRACTION99.8327759197
1.7899-1.86160.1208139807192130.09683787131323967X-RAY DIFFRACTION99.9043977055
1.8616-1.94630.1146322733442070.1030809292613970X-RAY DIFFRACTION99.8804399809
1.9463-2.04890.1096782662911950.1040661065634012X-RAY DIFFRACTION99.9762357414
2.0489-2.17730.1255640938612230.1009424846733970X-RAY DIFFRACTION99.8808956646
2.1773-2.34540.1222185221950.1101352856383988X-RAY DIFFRACTION99.9044662049
2.3454-2.58140.1226840998472150.1196450550464005X-RAY DIFFRACTION99.5517810804
2.5814-2.95490.1448338156252290.1337165150234004X-RAY DIFFRACTION99.7643176997
2.9549-3.72260.1402236161321970.1281479353094080X-RAY DIFFRACTION99.7667366457
3.7226-48.53380.1537334666582440.1431350298334178X-RAY DIFFRACTION99.4378232516

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