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- PDB-6hfj: Human dihydroorotase mutant F1563A co-crystallized with carbamoyl... -

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Basic information

Entry
Database: PDB / ID: 6hfj
TitleHuman dihydroorotase mutant F1563A co-crystallized with carbamoyl aspartate at pH 7.5
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 / glutamine metabolic process / response to starvation / response to amine / response to testosterone / 'de novo' UMP biosynthetic process / animal organ regeneration / 'de novo' pyrimidine nucleobase biosynthetic process / 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 / identical protein binding / membrane / 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 / 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 / Glutamine amidotransferase / Aspartate/ornithine carbamoyltransferase superfamily / Glutamine amidotransferase class-I / Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain / Aspartate/ornithine carbamoyltransferase, carbamoyl-P binding domain / 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: 1.2 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 / refine_hist / 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_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_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 / _refine_hist.d_res_high / _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_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)43,3989
Polymers42,8401
Non-polymers5588
Water8,269459
1
A: CAD protein
hetero molecules

A: CAD protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,79518
Polymers85,6802
Non-polymers1,11616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area5170 Å2
ΔGint-321 kcal/mol
Surface area25230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.932, 158.887, 60.923
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-1906-

FMT

21A-1906-

FMT

31A-2353-

HOH

41A-2406-

HOH

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Components

#1: Protein CAD protein


Mass: 42839.922 Da / Num. of mol.: 1 / Mutation: F1563A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAD / 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.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
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 7.5

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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: Jan 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→35.9234288569 Å / Num. obs: 123335 / % possible obs: 99.4 % / Redundancy: 6.3 % / Biso Wilson estimate: 13.8810002039 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.049 / Net I/σ(I): 18.9
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 12074 / CC1/2: 0.86 / Rrim(I) all: 0.684 / % possible all: 98.1

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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: 1.2→35.9234288569 Å / SU ML: 0.0928847723015 / Cross valid method: FREE R-VALUE / σ(F): 1.34101351104 / Phase error: 15.2037558859
RfactorNum. reflection% reflection
Rfree0.147839191913 6164 4.99979721783 %
Rwork0.128489200228 --
obs0.129473369082 123285 99.3504766663 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.2060635109 Å2
Refinement stepCycle: LAST / Resolution: 1.2→35.9234288569 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2776 0 24 465 3265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009966417467642985
X-RAY DIFFRACTIONf_angle_d1.154098190614094
X-RAY DIFFRACTIONf_chiral_restr0.107385522809461
X-RAY DIFFRACTIONf_plane_restr0.00847051522948542
X-RAY DIFFRACTIONf_dihedral_angle_d24.55632262681116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1994-1.21310.2355880335992210.2192050490643672X-RAY DIFFRACTION95.6276099239
1.2131-1.22730.2245536900851910.2079697408723896X-RAY DIFFRACTION99.2472073822
1.2273-1.24230.2288866258592000.2123150637193890X-RAY DIFFRACTION99.2718446602
1.2423-1.2580.242445788661830.1907979415013879X-RAY DIFFRACTION99.6565260059
1.258-1.27460.1933386217482040.1794413850153846X-RAY DIFFRACTION99.2647058824
1.2746-1.2920.1990210573952020.1662440137163898X-RAY DIFFRACTION99.7809686055
1.292-1.31050.1960731410841960.1667870305123876X-RAY DIFFRACTION99.6086105675
1.3105-1.33010.1973975409852170.1556565297693869X-RAY DIFFRACTION99.464459591
1.3301-1.35090.184670046521880.1453975609273916X-RAY DIFFRACTION99.8297251277
1.3509-1.3730.1621991233992080.1357488038893901X-RAY DIFFRACTION99.8299319728
1.373-1.39670.165545824882020.1292783295253879X-RAY DIFFRACTION99.706816516
1.3967-1.42210.1666786933742000.1295783386493915X-RAY DIFFRACTION99.8301795245
1.4221-1.44940.1569170924381860.1229124575833877X-RAY DIFFRACTION99.4127722046
1.4494-1.4790.1562042948972110.121818871633905X-RAY DIFFRACTION99.3722839208
1.479-1.51120.1465250360882070.1139584544933890X-RAY DIFFRACTION99.4176170832
1.5112-1.54630.1389070973831990.1081656155443898X-RAY DIFFRACTION99.7808085728
1.5463-1.5850.1463874935182280.105327669023847X-RAY DIFFRACTION99.6332518337
1.585-1.62790.1398635948481900.1055643457343938X-RAY DIFFRACTION99.5658465991
1.6279-1.67580.1399215914342200.1038608555613871X-RAY DIFFRACTION99.5135003649
1.6758-1.72980.1293286218872190.1007378823993911X-RAY DIFFRACTION99.7343636803
1.7298-1.79170.1171247077012030.0971901296683931X-RAY DIFFRACTION99.9274836838
1.7917-1.86340.1308588692592060.1033277133313941X-RAY DIFFRACTION99.7354497354
1.8634-1.94820.1141830955912070.1032188672263895X-RAY DIFFRACTION99.3220338983
1.9482-2.05090.1258462620421890.105434911363908X-RAY DIFFRACTION98.7943091391
2.0509-2.17940.1190325691992230.1034562532453929X-RAY DIFFRACTION99.6878751501
2.1794-2.34760.1434401220451910.1119362005213960X-RAY DIFFRACTION99.3537577788
2.3476-2.58380.1322221139192120.1230225884143929X-RAY DIFFRACTION99.4715349508
2.5838-2.95750.1302815554132230.1355875549523955X-RAY DIFFRACTION99.3106726884
2.9575-3.72560.1534299600911940.133595376073967X-RAY DIFFRACTION97.9058823529
3.7256-35.93950.1641046768332440.1518514241814132X-RAY DIFFRACTION99.4771538986

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