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

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Basic information

Entry
Database: PDB / ID: 9hdu
TitleOrotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with XMP at 1.0 Angstrom resolution
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
PROLINE / XANTHOSINE-5'-MONOPHOSPHATE / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsKirck, L.L. / 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 13, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6843
Polymers28,2041
Non-polymers4802
Water5,152286
1
A: Uridine 5'-monophosphate synthase
hetero molecules

A: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3686
Polymers56,4072
Non-polymers9614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area5220 Å2
ΔGint-33 kcal/mol
Surface area18730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.360, 116.690, 61.870
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-754-

HOH

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Components

#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)
References: UniProt: P11172, orotate phosphoribosyltransferase, orotidine-5'-phosphate decarboxylase
#2: Chemical ChemComp-XMP / XANTHOSINE-5'-MONOPHOSPHATE / 5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE


Mass: 365.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N4O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.48 Å3/Da / Density % sol: 50.31 %
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 EIGER2 X CdTe 16M / Detector: PIXEL / Date: Feb 27, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 1→44.64 Å / Num. obs: 148627 / % possible obs: 98.83 % / Redundancy: 10.2 % / CC1/2: 0.999 / Rrim(I) all: 0.06976 / Net I/σ(I): 15.69
Reflection shellResolution: 1→1.036 Å / Num. unique obs: 14556 / CC1/2: 0.506

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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→44.64 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 12.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1316 7431 5 %
Rwork0.1173 --
obs0.118 148585 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1→44.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 32 286 2285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012409
X-RAY DIFFRACTIONf_angle_d1.2413306
X-RAY DIFFRACTIONf_dihedral_angle_d14.85930
X-RAY DIFFRACTIONf_chiral_restr0.085368
X-RAY DIFFRACTIONf_plane_restr0.011440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.010.26452410.30454575X-RAY DIFFRACTION98
1.01-1.020.31422430.27324599X-RAY DIFFRACTION98
1.02-1.040.26892440.25074644X-RAY DIFFRACTION98
1.04-1.050.25042440.22784631X-RAY DIFFRACTION98
1.05-1.060.24482440.21194633X-RAY DIFFRACTION98
1.06-1.080.19752440.19134636X-RAY DIFFRACTION98
1.08-1.090.1992430.17844622X-RAY DIFFRACTION98
1.09-1.110.17522450.16174649X-RAY DIFFRACTION98
1.11-1.130.15622450.14784654X-RAY DIFFRACTION98
1.13-1.140.14512440.13984631X-RAY DIFFRACTION98
1.14-1.160.15732450.12854661X-RAY DIFFRACTION98
1.16-1.190.13932440.12314639X-RAY DIFFRACTION98
1.19-1.210.12942470.11244683X-RAY DIFFRACTION99
1.21-1.230.10722450.10554662X-RAY DIFFRACTION99
1.23-1.260.12742470.09854687X-RAY DIFFRACTION99
1.26-1.290.11032470.09354707X-RAY DIFFRACTION99
1.29-1.320.10732490.08924715X-RAY DIFFRACTION99
1.32-1.360.11252480.08594710X-RAY DIFFRACTION99
1.36-1.40.10482480.08284723X-RAY DIFFRACTION99
1.4-1.440.09352480.08264701X-RAY DIFFRACTION99
1.44-1.490.11032480.07914728X-RAY DIFFRACTION100
1.49-1.550.08872510.07524753X-RAY DIFFRACTION99
1.55-1.620.11472490.07774732X-RAY DIFFRACTION99
1.62-1.710.10592500.08564756X-RAY DIFFRACTION99
1.71-1.820.10532500.09364748X-RAY DIFFRACTION100
1.82-1.960.11412520.09494782X-RAY DIFFRACTION100
1.96-2.150.10922530.10194822X-RAY DIFFRACTION100
2.15-2.470.11792540.11144829X-RAY DIFFRACTION100
2.47-3.110.13482550.13054840X-RAY DIFFRACTION99
3.11-44.640.15162640.13585002X-RAY DIFFRACTION99

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