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- PDB-9hil: Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in ... -

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Basic information

Entry
Database: PDB / ID: 9hil
TitleOrotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with Cytidine-5'-monophosphate (CMP)
ComponentsUridine 5'-monophosphate synthase
KeywordsLYASE / Uridine 5'-monophosphate synthase Pyrimidine metabolism Homo sapiens
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 / 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-type TIM barrel
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKirck, L.L. / Santagostino, E. / Tittmann, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochemistry / Year: 2025
Title: Expected and Unexpected "Guests" at the Active Site of Human Orotidine 5'-Monophosphate Decarboxylase.
Authors: Kirck, L.L. / Santagostino, E. / Brandhoff, L. / Simeth, N.A. / Tittmann, K.
History
DepositionNov 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)56,8554
Polymers56,2092
Non-polymers6462
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-22 kcal/mol
Surface area19200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.180, 75.590, 119.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 28104.551 Da / Num. of mol.: 2
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)
References: UniProt: P11172, orotate phosphoribosyltransferase, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-C / CYTIDINE-5'-MONOPHOSPHATE


Type: RNA linking / Mass: 323.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N3O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
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: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 100 mM Tris/HCl pH 7.0, 1.7 - 1.9 M Ammonium sulfate, 10 mM Glutathion pH 8.0, 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: P14 (MX2) / Wavelength: 0.6888 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 7, 2024
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 1.6→48.02 Å / Num. obs: 74724 / % possible obs: 98.52 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rrim(I) all: 0.116 / Net I/σ(I): 14.31
Reflection shellResolution: 1.6→1.657 Å / Num. unique obs: 7393 / CC1/2: 0.756

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→48.02 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2295 3688 5 %
Rwork0.2037 --
obs0.205 73734 98.52 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→48.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3838 0 42 241 4121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054114
X-RAY DIFFRACTIONf_angle_d0.8055572
X-RAY DIFFRACTIONf_dihedral_angle_d16.9671553
X-RAY DIFFRACTIONf_chiral_restr0.065635
X-RAY DIFFRACTIONf_plane_restr0.006714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.34371400.3552677X-RAY DIFFRACTION100
1.62-1.640.34761440.33032717X-RAY DIFFRACTION100
1.64-1.670.39281400.33612662X-RAY DIFFRACTION100
1.67-1.690.3181430.31732710X-RAY DIFFRACTION100
1.69-1.720.35971430.3122712X-RAY DIFFRACTION100
1.72-1.750.32671410.28932686X-RAY DIFFRACTION100
1.75-1.780.33691440.27682722X-RAY DIFFRACTION100
1.78-1.810.33631410.26942672X-RAY DIFFRACTION100
1.81-1.840.28781430.242709X-RAY DIFFRACTION100
1.84-1.880.24851440.2142730X-RAY DIFFRACTION100
1.88-1.920.39671270.37082414X-RAY DIFFRACTION90
1.92-1.970.30891310.242496X-RAY DIFFRACTION92
1.97-2.020.24521440.19092725X-RAY DIFFRACTION100
2.02-2.070.21781440.19872729X-RAY DIFFRACTION100
2.07-2.130.23131420.19242701X-RAY DIFFRACTION100
2.13-2.20.22381430.19222725X-RAY DIFFRACTION100
2.2-2.280.36851220.31392320X-RAY DIFFRACTION85
2.28-2.370.24481430.1912709X-RAY DIFFRACTION100
2.37-2.480.19491440.18282725X-RAY DIFFRACTION100
2.48-2.610.22011450.18942747X-RAY DIFFRACTION100
2.61-2.770.25531430.19262724X-RAY DIFFRACTION100
2.77-2.990.22081440.19932734X-RAY DIFFRACTION99
2.99-3.290.18861470.19382797X-RAY DIFFRACTION100
3.29-3.760.19181450.16762767X-RAY DIFFRACTION100
3.76-4.740.16241490.15752818X-RAY DIFFRACTION100
4.74-48.020.21861520.19442918X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -0.0298 Å / Origin y: -7.1764 Å / Origin z: 1.302 Å
111213212223313233
T0.1561 Å2-0.0106 Å20.0005 Å2-0.3057 Å2-0.0105 Å2--0.207 Å2
L1.305 °20.0178 °2-0.1397 °2-0.458 °2-0.0933 °2--1.8847 °2
S0.0023 Å °0.0078 Å °0.1438 Å °0.0059 Å °-0.0349 Å °-0.0115 Å °-0.1252 Å °0.0974 Å °0.0411 Å °
Refinement TLS groupSelection details: all

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