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- PDB-6ftq: Crystal structure of human beta-ureidopropionase (beta-alanine sy... -

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Basic information

Entry
Database: PDB / ID: 6ftq
TitleCrystal structure of human beta-ureidopropionase (beta-alanine synthase) - mutant T299C
ComponentsBeta-ureidopropionase
KeywordsHYDROLASE / pyrimidine degradation / N-carbamyl-beta-alanine amidohydrolase / 5-fluorouracil metabolizing enzyme
Function / homology
Function and homology information


pyrimidine nucleoside catabolic process / beta-ureidopropionase / CMP catabolic process / UMP catabolic process / dCMP catabolic process / beta-alanine biosynthetic process via 3-ureidopropionate / beta-ureidopropionase activity / dUMP catabolic process / Pyrimidine catabolism / liver development ...pyrimidine nucleoside catabolic process / beta-ureidopropionase / CMP catabolic process / UMP catabolic process / dCMP catabolic process / beta-alanine biosynthetic process via 3-ureidopropionate / beta-ureidopropionase activity / dUMP catabolic process / Pyrimidine catabolism / liver development / protein homooligomerization / protein homotetramerization / in utero embryonic development / protein homodimerization activity / extracellular exosome / cytosol
Similarity search - Function
Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Beta-ureidopropionase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsDobritzsch, D. / Maurer, D.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Carl Tryggers FoundationCS14:111 Sweden
CitationJournal: Biochem. J. / Year: 2018
Title: Crystal structure and pH-dependent allosteric regulation of human beta-ureidopropionase, an enzyme involved in anticancer drug metabolism.
Authors: Maurer, D. / Lohkamp, B. / Krumpel, M. / Widersten, M. / Dobritzsch, D.
History
DepositionFeb 23, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-ureidopropionase


Theoretical massNumber of molelcules
Total (without water)43,8841
Polymers43,8841
Non-polymers00
Water3,747208
1
A: Beta-ureidopropionase

A: Beta-ureidopropionase


  • defined by author&software
  • Evidence: gel filtration, the native enzyme occurs in several oligomeric states, the T299C variant exclusively as homodimer, as determined by gel filtration, native PAGE, static light scattering, and ...Evidence: gel filtration, the native enzyme occurs in several oligomeric states, the T299C variant exclusively as homodimer, as determined by gel filtration, native PAGE, static light scattering, and the crystal structure
  • 87.8 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)87,7672
Polymers87,7672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area6170 Å2
ΔGint-46 kcal/mol
Surface area26080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.815, 104.244, 102.808
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-527-

HOH

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Components

#1: Protein Beta-ureidopropionase / / BUP-1 / Beta-alanine synthase / N-carbamoyl-beta-alanine amidohydrolase


Mass: 43883.691 Da / Num. of mol.: 1 / Mutation: T299C
Source method: isolated from a genetically manipulated source
Details: the first 6 amino acids are a remainder of a cleaved His-tag C233 is oxidized to cysteine sulfinic acid T299 is mutated to cysteine
Source: (gene. exp.) Homo sapiens (human) / Gene: UPB1, BUP1 / Plasmid: pET151/D-TOPO / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): AI / References: UniProt: Q9UBR1, beta-ureidopropionase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.66 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: 16% (w/v) PEG 3350 0.1 M HEPES pH 7.75 300 mM NaSCN 3 mg/ml enzyme variant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.08→28.63 Å / Num. obs: 28448 / % possible obs: 99.6 % / Redundancy: 13.4 % / Biso Wilson estimate: 37.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.126 / Rpim(I) all: 0.036 / Rrim(I) all: 0.131 / Net I/σ(I): 14.6
Reflection shellResolution: 2.08→2.13 Å / Redundancy: 13 % / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 2096 / CC1/2: 0.892 / Rpim(I) all: 0.232 / Rrim(I) all: 0.847 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2VHH

2vhh


Resolution: 2.08→28.1 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.925 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.137 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1991 1453 5.1 %RANDOM
Rwork0.17539 ---
obs0.17656 26915 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 35.248 Å2
Baniso -1Baniso -2Baniso -3
1--1.84 Å2-0 Å20 Å2
2--2.32 Å2-0 Å2
3----0.48 Å2
Refinement stepCycle: 1 / Resolution: 2.08→28.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2621 0 0 208 2829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192711
X-RAY DIFFRACTIONr_bond_other_d0.0020.022474
X-RAY DIFFRACTIONr_angle_refined_deg1.3221.943682
X-RAY DIFFRACTIONr_angle_other_deg0.91835725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2735335
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.18923.233133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3415441
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1531524
X-RAY DIFFRACTIONr_chiral_restr0.0760.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213042
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02586
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6191.7071331
X-RAY DIFFRACTIONr_mcbond_other0.6191.7071330
X-RAY DIFFRACTIONr_mcangle_it1.1122.5531660
X-RAY DIFFRACTIONr_mcangle_other1.1112.5531661
X-RAY DIFFRACTIONr_scbond_it0.5221.7861380
X-RAY DIFFRACTIONr_scbond_other0.5221.7871377
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.9062.6582018
X-RAY DIFFRACTIONr_long_range_B_refined4.95620.9473033
X-RAY DIFFRACTIONr_long_range_B_other4.85320.3862992
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.08→2.134 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 113 -
Rwork0.219 1957 -
obs--99.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.86891.7142-2.77565.4762-2.22476.7811-0.1699-0.0628-0.5977-0.1455-0.1001-0.50590.49830.73230.270.21180.0698-0.0440.17540.00530.13899.587-44.8228-5.3623
24.8823-0.1855-0.95722.0126-0.15432.4052-0.0452-0.1125-0.25620.1750.10360.33250.1105-0.2233-0.05850.1119-0.00110.01070.12790.01410.0734-3.7884-34.41950.2332
34.1143-0.0365-0.66981.31750.02531.5966-0.0575-0.19850.30020.06620.08450.1021-0.2858-0.2525-0.0270.13260.01270.00660.1852-0.03860.0565-8.389-21.74870.4372
41.23160.03920.40592.9676-0.18413.0501-0.01250.0156-0.0021-0.0153-0.00260.12680.0451-0.05280.01510.03730.0006-0.00330.0887-0.00950.0068-0.7454-30.5144-13.7879
51.48420.0649-2.58863.36692.00426.02860.16780.23850.1641-0.37-0.15680.4122-0.7864-0.4156-0.0110.4137-0.0581-0.05390.18920.03960.2975-0.848-11.7739-33.9955
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 66
2X-RAY DIFFRACTION2A67 - 127
3X-RAY DIFFRACTION3A128 - 201
4X-RAY DIFFRACTION4A212 - 356
5X-RAY DIFFRACTION5A357 - 384

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