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

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Basic information

Entry
Database: PDB / ID: 9hdy
TitleOrotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with 2'-Thiouridine-5'-monophosphate (USP)
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
: / 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 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,5442
Polymers28,2041
Non-polymers3401
Water2,882160
1
A: Uridine 5'-monophosphate synthase
hetero molecules

A: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0884
Polymers56,4072
Non-polymers6802
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area3890 Å2
ΔGint-25 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.830, 117.010, 62.230
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-737-

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-A1IT3 / 2'-thiouridine-5'-monophosphate / ((2R,3R,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3-hydroxy-4-mercaptotetrahydrofuran-2-yl)methyl dihydrogen phosphate / [(2~{R},3~{R},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-4-sulfanyl-oxolan-2-yl]methyl dihydrogen phosphate / 2'-SH UMP


Mass: 340.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O8PS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.51 Å3/Da / Density % sol: 51.03 %
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: 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→42.63 Å / Num. obs: 37800 / % possible obs: 96.31 % / Redundancy: 7.2 % / CC1/2: 0.998 / Rrim(I) all: 0.1186 / Net I/σ(I): 10.44
Reflection shellResolution: 1.6→1.657 Å / Num. unique obs: 3716 / CC1/2: 0.561

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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→42.63 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2421 1824 5 %
Rwork0.2213 --
obs0.2223 36455 96.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→42.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 21 160 2148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112236
X-RAY DIFFRACTIONf_angle_d0.9713055
X-RAY DIFFRACTIONf_dihedral_angle_d15.558852
X-RAY DIFFRACTIONf_chiral_restr0.078343
X-RAY DIFFRACTIONf_plane_restr0.009404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.32461430.33812721X-RAY DIFFRACTION100
1.64-1.690.34651430.31922720X-RAY DIFFRACTION100
1.69-1.750.33681430.30032729X-RAY DIFFRACTION99
1.75-1.810.30431440.27092738X-RAY DIFFRACTION100
1.81-1.880.25381440.23422734X-RAY DIFFRACTION100
1.88-1.970.52911110.44542093X-RAY DIFFRACTION77
1.97-2.070.21781460.20282774X-RAY DIFFRACTION100
2.07-2.20.21581440.20232740X-RAY DIFFRACTION100
2.2-2.370.43431140.35672152X-RAY DIFFRACTION78
2.37-2.610.19341460.20462784X-RAY DIFFRACTION100
2.61-2.990.2261460.20542756X-RAY DIFFRACTION100
2.99-3.760.20071460.18422776X-RAY DIFFRACTION98
3.76-42.630.18721540.17232914X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 12.0815 Å / Origin y: 15.7235 Å / Origin z: 29.5558 Å
111213212223313233
T0.1965 Å2-0.0318 Å2-0.0039 Å2-0.1082 Å20.0146 Å2--0.1201 Å2
L0.9467 °20.1493 °20.021 °2-1.5106 °20.0559 °2--1.3359 °2
S-0.016 Å °0.0069 Å °0.0122 Å °-0.0581 Å °0.0443 Å °-0.0699 Å °-0.1105 Å °0.1015 Å °-0.0289 Å °
Refinement TLS groupSelection details: all

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