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- PDB-7asq: Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in ... -

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Basic information

Entry
Database: PDB / ID: 7asq
TitleOrotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with the reaction product UMP at 0.95 Angstrom resolution
ComponentsUridine 5'-monophosphate synthase
KeywordsLYASE / OMPD / UMPS / UMP
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 / identical protein binding / nucleus / cytoplasm / cytosol
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-type TIM barrel
Similarity search - Domain/homology
URIDINE-5'-MONOPHOSPHATE / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsRindfleisch, S. / Rabe von Pappenheim, F.
CitationJournal: Nat Catal / Year: 2022
Title: Ground-state destabilization by electrostatic repulsion is not a driving force in orotidine-5-monophosphate decarboxylase catalysis
Authors: Rindfleisch, S. / Krull, M. / Uranga, J. / Schmidt, T. / Rabe von Pappenheim, F. / Kirck, L.L. / Balouri, A. / Schneider, T. / Chari, A. / Kluger, R. / Bourenkov, G. / Diederichsen, U. / ...Authors: Rindfleisch, S. / Krull, M. / Uranga, J. / Schmidt, T. / Rabe von Pappenheim, F. / Kirck, L.L. / Balouri, A. / Schneider, T. / Chari, A. / Kluger, R. / Bourenkov, G. / Diederichsen, U. / Mata, R.A. / Tittmann, K.
History
DepositionOct 28, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8356
Polymers28,2041
Non-polymers6315
Water5,963331
1
A: Uridine 5'-monophosphate synthase
hetero molecules

A: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,67012
Polymers56,4072
Non-polymers1,26310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area6460 Å2
ΔGint-90 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.670, 116.860, 61.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-856-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Uridine 5'-monophosphate synthase / UMP synthase / Orotidine-5'-monophosphate decarboxylase


Mass: 28203.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UMPS, OK/SW-cl.21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): SoluBL21
References: UniProt: P11172, orotate phosphoribosyltransferase, orotidine-5'-phosphate decarboxylase

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Non-polymers , 5 types, 336 molecules

#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-U5P / URIDINE-5'-MONOPHOSPHATE


Mass: 324.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O9P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris/HCl pH 7.0, 1.7 - 1.9 M Ammonium sulfate, 10 mM Glutathion, 5% (w/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.85 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.85 Å / Relative weight: 1
ReflectionResolution: 0.95→38.83 Å / Num. obs: 174560 / % possible obs: 99.2 % / Redundancy: 6.489 % / Biso Wilson estimate: 10.454 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.071 / Χ2: 0.967 / Net I/σ(I): 12.38 / Num. measured all: 1132720 / Scaling rejects: 38
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
0.95-16.310.8391.7115363324881243490.7710.91497.9
1-1.16.3880.4613.2923502437273367900.9260.50298.7
1.1-1.26.3040.2575.9116209525885257130.9710.28199.3
1.2-1.36.7350.1998.0212483118607185340.9830.21699.6
1.3-1.46.550.1599.968921513640136210.9880.17399.9
1.4-1.56.3890.12712.086557910285102640.9910.13999.8
1.5-56.6780.03930.9129354544042439590.9990.04299.8
5-106.790.02559.477836115411540.9990.027100
10-205.7580.02460.89041591570.9990.02698.7
20-38.833.0530.02142.355827190.9990.02570.4

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QCD

2qcd


Resolution: 0.95→38.83 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 11.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1199 8727 5 %
Rwork0.107 165814 -
obs0.1076 174541 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 46.15 Å2 / Biso mean: 10.9568 Å2 / Biso min: 4.57 Å2
Refinement stepCycle: final / Resolution: 0.95→38.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1963 0 60 344 2367
Biso mean--11.16 23.75 -
Num. residues----256
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.95-0.960.26352830.25425387567097
0.96-0.970.23982840.24265396568098
0.97-0.980.23692850.2225407569298
0.98-10.22022850.20995415570098
1-1.010.21472870.19615459574699
1.01-1.020.20932860.18415430571699
1.02-1.040.17622880.16595468575698
1.04-1.050.16772850.14825421570699
1.05-1.070.14782880.13965470575899
1.07-1.090.13972880.12285488577699
1.09-1.110.11762870.1185446573399
1.11-1.130.12312920.10685553584599
1.13-1.150.11292890.10355489577899
1.15-1.170.11712900.0995510580099
1.17-1.20.10842910.0955517580899
1.2-1.220.11242910.090755365827100
1.22-1.260.10452910.088455335824100
1.26-1.290.112920.086155385830100
1.29-1.330.09562910.082455395830100
1.33-1.370.08832930.08255675860100
1.37-1.420.10172930.079455615854100
1.42-1.480.09142910.078455415832100
1.48-1.540.08862930.073255675860100
1.54-1.620.08312950.073656055900100
1.62-1.730.09482950.081355865881100
1.73-1.860.09642940.086255995893100
1.86-2.050.10352950.087556045899100
2.05-2.340.10352970.094656465943100
2.34-2.950.11643000.10756895989100
2.95-38.830.13893080.12758476155100

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