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- PDB-9hdt: Variant T321N of Orotidine 5'-monophosphate decarboxylase-domain ... -

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Basic information

Entry
Database: PDB / ID: 9hdt
TitleVariant T321N of Orotidine 5'-monophosphate decarboxylase-domain of human UMPS in complex with Deoxyuridine-5'-monophosphate (Deoxy UMP) at 1.3 Angstroms 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
2'-DEOXYURIDINE-5'-MONOPHOSPHATE / PROLINE / Uridine 5'-monophosphate synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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)28,6403
Polymers28,2171
Non-polymers4232
Water5,350297
1
A: Uridine 5'-monophosphate synthase
hetero molecules

A: Uridine 5'-monophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2806
Polymers56,4332
Non-polymers8474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area3760 Å2
ΔGint-23 kcal/mol
Surface area19100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.090, 116.310, 62.180
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-673-

HOH

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Components

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


Mass: 28216.680 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Asparagine inserted instead of Thr321 / 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-DU / 2'-DEOXYURIDINE-5'-MONOPHOSPHATE


Type: DNA linking / Mass: 308.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H13N2O8P / 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.: 297 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
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: Nov 10, 2022
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6888 Å / Relative weight: 1
ReflectionResolution: 1.3→32.42 Å / Num. obs: 69652 / % possible obs: 99.84 % / Redundancy: 6.8 % / CC1/2: 0.999 / Rrim(I) all: 0.09726 / Net I/σ(I): 12.28
Reflection shellResolution: 1.3→1.347 Å / Num. unique obs: 6885 / CC1/2: 0.717

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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: 1.3→32.42 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1513 3482 5 %
Rwork0.1259 --
obs0.1272 69633 99.85 %
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→32.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1968 0 28 297 2293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092333
X-RAY DIFFRACTIONf_angle_d1.1563195
X-RAY DIFFRACTIONf_dihedral_angle_d14.687904
X-RAY DIFFRACTIONf_chiral_restr0.079352
X-RAY DIFFRACTIONf_plane_restr0.01429
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.320.26841380.24472629X-RAY DIFFRACTION100
1.32-1.340.28851370.23372584X-RAY DIFFRACTION100
1.34-1.360.2481380.22582621X-RAY DIFFRACTION99
1.36-1.380.28111370.22112615X-RAY DIFFRACTION100
1.38-1.40.25781380.2092622X-RAY DIFFRACTION100
1.4-1.420.25311380.19822607X-RAY DIFFRACTION100
1.42-1.450.23491370.18712621X-RAY DIFFRACTION100
1.45-1.480.2071390.17292622X-RAY DIFFRACTION100
1.48-1.510.1961380.16032637X-RAY DIFFRACTION100
1.51-1.540.19671380.13642603X-RAY DIFFRACTION100
1.54-1.580.17551380.12922634X-RAY DIFFRACTION100
1.58-1.620.17571400.11392652X-RAY DIFFRACTION100
1.62-1.660.13591380.11442626X-RAY DIFFRACTION100
1.66-1.710.15041390.10782628X-RAY DIFFRACTION100
1.71-1.760.15591390.10332650X-RAY DIFFRACTION100
1.76-1.830.1441390.10292629X-RAY DIFFRACTION100
1.83-1.90.12161390.09732658X-RAY DIFFRACTION100
1.9-1.990.14861400.09462658X-RAY DIFFRACTION100
1.99-2.090.15481380.09882619X-RAY DIFFRACTION100
2.09-2.220.14231410.09772681X-RAY DIFFRACTION100
2.22-2.390.13521400.09952660X-RAY DIFFRACTION100
2.39-2.640.1161410.10522673X-RAY DIFFRACTION100
2.64-3.020.15531420.12282692X-RAY DIFFRACTION100
3.02-3.80.13061420.11992706X-RAY DIFFRACTION100
3.8-32.420.11811480.13522824X-RAY DIFFRACTION99

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