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- PDB-3ewu: D312N mutant of human orotidyl-5'-monophosphate decarboxylase in ... -

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Basic information

Entry
Database: PDB / ID: 3ewu
TitleD312N mutant of human orotidyl-5'-monophosphate decarboxylase in complex with 6-acetyl-UMP, covalent adduct
ComponentsOrotidine-5'-phosphate decarboxylase
KeywordsLYASE / decarboxylation / unusual catalysis / tim barrel / Decarboxylase / Disease mutation / Glycosyltransferase / Multifunctional enzyme / Pyrimidine biosynthesis / Transferase
Function / homology
Function and homology information


UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / orotidine-5'-phosphate decarboxylase / UDP biosynthetic process / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process ...UMP biosynthetic process / orotate phosphoribosyltransferase / orotate phosphoribosyltransferase activity / pyrimidine nucleobase biosynthetic process / Pyrimidine biosynthesis / orotidine-5'-phosphate decarboxylase / UDP biosynthetic process / orotidine-5'-phosphate decarboxylase activity / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / lactation / female pregnancy / cellular response to xenobiotic stimulus / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / Purine/pyrimidine phosphoribosyl transferases signature. / Orotidine 5'-phosphate decarboxylase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Phosphoribosyl transferase domain ...Orotate phosphoribosyl transferase domain / Orotate phosphoribosyltransferase / Purine/pyrimidine phosphoribosyl transferases signature. / Orotidine 5'-phosphate decarboxylase / Orotidine 5'-phosphate decarboxylase, active site / Orotidine 5'-phosphate decarboxylase active site. / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
6-ethyluridine 5'-phosphate / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHeinrich, D. / Wittmann, J. / Diederichsen, U. / Rudolph, M.
CitationJournal: Chemistry / Year: 2009
Title: Lys314 is a nucleophile in non-classical reactions of orotidine-5'-monophosphate decarboxylase
Authors: Heinrich, D. / Diederichsen, U. / Rudolph, M.G.
History
DepositionOct 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Orotidine-5'-phosphate decarboxylase
B: Orotidine-5'-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4906
Polymers56,5982
Non-polymers8934
Water9,242513
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-22.3 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.410, 61.690, 70.810
Angle α, β, γ (deg.)90.00, 112.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Orotidine-5'-phosphate decarboxylase / OMPdecase


Mass: 28298.758 Da / Num. of mol.: 2 / Fragment: UNP residues 224-480 / Mutation: D312N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UMPS / Plasmid: pETM-30 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: P11172, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-UEP / 6-ethyluridine 5'-phosphate / 6-ethyl-UMP


Mass: 352.234 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17N2O9P
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 513 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris-HCl pH 8.0, 1.8 M (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 300.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→44.3 Å / Num. obs: 72838 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 9
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.531 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2657 / % possible all: 99.1

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Processing

Software
NameVersionClassification
COMOphasing
REFMAC5.5.0057refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→38.78 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.066 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19614 3553 5 %RANDOM
Rwork0.16299 ---
obs0.16465 67721 97.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.955 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å22.03 Å2
2---0.75 Å20 Å2
3---1.65 Å2
Refinement stepCycle: LAST / Resolution: 1.6→38.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3932 0 57 513 4502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224306
X-RAY DIFFRACTIONr_bond_other_d0.0010.022959
X-RAY DIFFRACTIONr_angle_refined_deg1.5921.9965869
X-RAY DIFFRACTIONr_angle_other_deg0.98237285
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9285587
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92523.82178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20515811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6081532
X-RAY DIFFRACTIONr_chiral_restr0.0970.2677
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024801
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02843
X-RAY DIFFRACTIONr_mcbond_it0.9661.52663
X-RAY DIFFRACTIONr_mcbond_other0.2951.51100
X-RAY DIFFRACTIONr_mcangle_it1.7224304
X-RAY DIFFRACTIONr_scbond_it2.86131643
X-RAY DIFFRACTIONr_scangle_it4.6794.51526
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 242 -
Rwork0.344 4588 -
obs--90.52 %

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